Genomes and Genes
Experts and Doctors on dna in Baton Rouge, Louisiana, United States
Locale: Baton Rouge, Louisiana, United States
- Triant D, Whitehead A. Simultaneous extraction of high-quality RNA and DNA from small tissue samples. J Hered. 2009;100:246-50 pubmed publisher..Although these extraction trials were conducted on fish embryos, they can be potentially applied to small samples that typically do not yield high concentrations of nucleic acids. ..
- Lee W, Lee Y, Lee J, Davis L, Deininger P, Soper S. Cross-talk-free dual-color fluorescence cross-correlation spectroscopy for the study of enzyme activity. Anal Chem. 2010;82:1401-10 pubmed publisher..In all cases, no spectral leakage from single-molecule events into inappropriate color channels was observed. ..
- Grove A, Wilkinson S. Differential DNA binding and protection by dimeric and dodecameric forms of the ferritin homolog Dps from Deinococcus radiodurans. J Mol Biol. 2005;347:495-508 pubmed publisher..While dodecameric Dps-1 does bind DNA, resulting in formation of large aggregates, cooperative DNA binding by dimeric Dps-1 leads to formation of protein-DNA complexes of finite stoichiometry...
- Mukherjee A, Sokunbi A, Grove A. DNA protection by histone-like protein HU from the hyperthermophilic eubacterium Thermotoga maritima. Nucleic Acids Res. 2008;36:3956-68 pubmed publisher..We suggest that T. maritima HU serves an architectural function when associating with a single 35 bp site, but generates a very stable and compact aggregate at higher protein concentrations that organizes and protects the genomic DNA. ..
- Joubert A, Byrd A, LiCata V. Global conformations, hydrodynamics, and X-ray scattering properties of Taq and Escherichia coli DNA polymerases in solution. J Biol Chem. 2003;278:25341-7 pubmed..Further, the radius of gyration, and hence the global conformation of Taq polymerase, is not altered by the binding of either matched primer template DNA or ddATP. ..
- Chandler J, Canal A, Paul J, Moser E. Collection frequency affects percent Y-chromosome bearing sperm, sperm head area and quality of bovine ejaculates. Theriogenology. 2002;57:1327-46 pubmed..Maximization of %Y-CDBS variation between ejaculate and its identification by PCR would allow ejaculate selection to be used to the alter the sex ratio in producers' calf crops...
- ..Also, this shortening suggests that the DNA recognition by YY1 is mediated through the concerted, but not modular, contribution by its four zinc finger units. ..
- Schoeller E, Husseneder C, Allison J. Molecular evidence of facultative intraguild predation by Monochamus titillator larvae (Coleoptera: Cerambycidae) on members of the southern pine beetle guild. Naturwissenschaften. 2012;99:913-24 pubmed publisher..Additionally, this study demonstrates the capabilities of PCR in elucidating the interactions of cryptic forest insects and provides a tool to better understand mechanisms driving southern pine beetle guild population fluctuations...
- Faulk C, Kim J. YY1's DNA-binding motifs in mammalian olfactory receptor genes. BMC Genomics. 2009;10:576 pubmed publisher..YY1, or YY1-related transcription factors, may help regulate olfactory receptor genes. Furthermore, the protein-coding regions of vertebrate genes can contain cis-regulatory elements for transcription factor binding as well as codons. ..
- Bouchard C, Rankinen T, Chagnon Y, Rice T, Perusse L, Gagnon J, et al. Genomic scan for maximal oxygen uptake and its response to training in the HERITAGE Family Study. J Appl Physiol (1985). 2000;88:551-9 pubmed..These chromosomal regions harbor many genes that may qualify as candidate genes for these quantitative traits. They should be investigated in this and other cohorts...
- Yacoub A, Kelley M, Deutsch W. Drosophila ribosomal protein PO contains apurinic/apyrimidinic endonuclease activity. Nucleic Acids Res. 1996;24:4298-303 pubmed..Other roles beyond DNA repair seem possible, however, since GST-PO also exhibited significant nuclease activity for both single- and double-stranded DNA. ..
- Sinville R, Soper S. High resolution DNA separations using microchip electrophoresis. J Sep Sci. 2007;30:1714-28 pubmed
- Tsihlis N, Grove A. The Saccharomyces cerevisiae RNA polymerase III recruitment factor subunits Brf1 and Bdp1 impose a strict sequence preference for the downstream half of the TATA box. Nucleic Acids Res. 2006;34:5585-93 pubmed..We suggest that the selected T*A base pair step at the downstream end of the 8 bp TBP site may provide a DNA flexure that promotes TFIIIB-DNA complex formation. ..
- Xiao L, Williams A, Grove A. The C-terminal domain of yeast high mobility group protein HMO1 mediates lateral protein accretion and in-phase DNA bending. Biochemistry. 2010;49:4051-9 pubmed publisher..This mode of binding is reminiscent of that proposed for the mammalian RNA polymerase I transcription factor UBF. ..
- Valdez B, Chen Z, Sosa M, Younathan E, Chang S. Human 6-phosphofructo-1-kinase gene has an additional intron upstream of start codon. Gene. 1989;76:167-9 pubmed..The available sequence of the two cDNAs shows 256 nt differences. Surprisingly, 71% of these sites are A's and T's in the human cDNA and C's and G's in the rabbit gene. ..
- Wilkinson S, Grove A. Negative cooperativity of uric acid binding to the transcriptional regulator HucR from Deinococcus radiodurans. J Mol Biol. 2005;350:617-30 pubmed..Mechanistic considerations suggest that HucR is regulated by uric acid to maintain optimal cellular levels of this scavenger of free radicals in response to oxidative stress and DNA damage. ..
- Kamau E, Bauerle K, Grove A. The Saccharomyces cerevisiae high mobility group box protein HMO1 contains two functional DNA binding domains. J Biol Chem. 2004;279:55234-40 pubmed..The unique DNA binding properties of HMO1 are consistent with global roles in the maintenance of chromatin structure. ..
- Kim J, Hinz A, Choo J, Stubbs L, Kim J. YY1 as a controlling factor for the Peg3 and Gnas imprinted domains. Genomics. 2007;89:262-9 pubmed..YY1 knockdown also resulted in changes in the expression levels of Xist and Snrpn. These results support the idea that YY1 plays a major role, as a trans factor, in the control of these imprinted domains. ..
- Kim D, Shih D, Cho D, Swenson D. Helix-stabilizing compounds CC-1065 and U-71,184 bind to RNA-DNA and DNA-DNA duplexes containing modified internucleotide linkages and stabilize duplexes against thermal melting. Antisense Res Dev. 1995;5:49-57 pubmed..The results show that CC-1065 and U-71,184 are capable of binding and stabilizing a variety of nucleic acid duplexes. These agents or their analogs may become useful ligands for antisense oligonucleotide applications. ..
- Wilkinson S, Grove A. HucR, a novel uric acid-responsive member of the MarR family of transcriptional regulators from Deinococcus radiodurans. J Biol Chem. 2004;279:51442-50 pubmed..radiodurans. Since uric acid is a scavenger of reactive oxygen species, we hypothesize that HucR is a participant in the intrinsic resistance of D. radiodurans to high levels of oxidative stress. ..
- Hedges D, Callinan P, Cordaux R, Xing J, Barnes E, Batzer M. Differential alu mobilization and polymorphism among the human and chimpanzee lineages. Genome Res. 2004;14:1068-75 pubmed..We propose a population-based model to account for the observed fluctuation in Alu retroposition rates across primate taxa...
- Vandergrifft E, Horohov D. Molecular cloning and expression of equine interleukin 2. Vet Immunol Immunopathol. 1993;39:395-406 pubmed..Specific substitutions in those regions associated with p55 and p75 binding appear to account for this species-specifity. ..
- Giraldo A, Hylan D, Ballard C, Purpera M, Vaught T, Lynn J, et al. Effect of epigenetic modifications of donor somatic cells on the subsequent chromatin remodeling of cloned bovine embryos. Biol Reprod. 2008;78:832-40 pubmed publisher..Furthermore, aberrant DNMT1 expression may partially contribute to the inefficient nuclear reprogramming observed in cloned embryos. ..
- Truett G, Heeger P, Mynatt R, Truett A, Walker J, Warman M. Preparation of PCR-quality mouse genomic DNA with hot sodium hydroxide and tris (HotSHOT). Biotechniques. 2000;29:52, 54 pubmed
- Singh V, Ganesh L, Cunningham M, Shane B. Comparison of the mutant frequencies and mutation spectra of three non-genotoxic carcinogens, oxazepam, phenobarbital, and Wyeth 14,643, at the lambdacII locus in Big Blue transgenic mice. Biochem Pharmacol. 2001;62:685-92 pubmed..Despite this hypersensitive region of the gene, our findings suggest that the cII locus is less sensitive than the lacI locus to mutation induction by non-DNA reactive carcinogens. ..
- Yang D, Jiang X, Elliott R, Head J. Inhibition of growth of human breast carcinoma cells by an antisense oligonucleotide targeted to the transferrin receptor gene. Anticancer Res. 2001;21:1777-87 pubmed
- Ray S, Grove A. The yeast high mobility group protein HMO2, a subunit of the chromatin-remodeling complex INO80, binds DNA ends. Nucleic Acids Res. 2009;37:6389-99 pubmed publisher..The remarkable ability of HMO2 to protect DNA from exonucleolytic cleavage, combined with reports that HMO2 arrives early at DNA DSBs, suggests that HMO2 may play a role in DSB repair beyond INO80 recruitment. ..
- Walker J, Hughes D, Anders B, Shewale J, Sinha S, Batzer M. Quantitative intra-short interspersed element PCR for species-specific DNA identification. Anal Biochem. 2003;316:259-69 pubmed..The SINE-based PCR methods we report here are species-specific, are highly sensitive, and will improve the detection limits for DNA sequences derived from these species. ..
- Fossett N, Byrne B, Tucker A, Arbour Reily P, Chang S, Lee W. Mutation spectrum of 2-chloroethyl methanesulfonate in Drosophila melanogaster premeiotic germ cells. Mutat Res. 1995;331:213-24 pubmed..Consequently, 2ClEMS, EDC and EDB may induce a specific mutation in premeiotic germ cells. ..
- Lahiri R, Randhawa B, Krahenbuhl J. Infection of mouse macrophages with viable Mycobacterium leprae does not induce apoptosis. J Infect Dis. 2010;201:1736-42 pubmed publisher..leprae. The results strongly suggest that the viability and purity of the leprosy bacilli used for in vitro studies determines the extent of apoptosis observed in infected host cells. ..
- Hegde V, Kelley M, Xu Y, Mian I, Deutsch W. Conversion of the bifunctional 8-oxoguanine/beta-delta apurinic/apyrimidinic DNA repair activities of Drosophila ribosomal protein S3 into the human S3 monofunctional beta-elimination catalyst through a single amino acid change. J Biol Chem. 2001;276:27591-6 pubmed
- Lee W, Obubuafo A, Lee Y, Davis L, Soper S. Single-pair fluorescence resonance energy transfer (spFRET) for the high sensitivity analysis of low-abundance proteins using aptamers as molecular recognition elements. J Fluoresc. 2010;20:203-13 pubmed publisher..We also demonstrate that the technique can discriminate thrombin molecules from its analogue prothrombin. The analytical sensitivity was >200-fold better than an ensemble measurement. ..
- Bauerle K, Kamau E, Grove A. Interactions between N- and C-terminal domains of the Saccharomyces cerevisiae high-mobility group protein HMO1 are required for DNA bending. Biochemistry. 2006;45:3635-45 pubmed..Taken together, our data suggest that interactions between box A and the C-terminal tail induce a conformation that is required for DNA bending. ..
- Ghosh S, Grove A. Histone-like protein HU from Deinococcus radiodurans binds preferentially to four-way DNA junctions. J Mol Biol. 2004;337:561-71 pubmed
- Benson B, Meades G, Grove A, Waldrop G. DNA inhibits catalysis by the carboxyltransferase subunit of acetyl-CoA carboxylase: implications for active site communication. Protein Sci. 2008;17:34-42 pubmed..An important mechanistic implication of these observations is that the dual active sites of ACC are functionally connected. ..
- Deutsch W, Hegde V. Analysis of DNA strand cleavage at abasic sites. Methods Mol Biol. 2005;291:39-46 pubmed..Here we describe a method for analyzing the manner in which repair endonucleases differ in the way they create nicks in DNA and how to distinguish between them using cellular crude extracts. ..
- Sheldon F, Whittingham L, Moyle R, Slikas B, Winkler D. Phylogeny of swallows (Aves: Hirundinidae) estimated from nuclear and mitochondrial DNA sequences. Mol Phylogenet Evol. 2005;35:254-70 pubmed..The final group of hirundinines, the basal relicts, consists of a sister pair, the Australian Cheramoeca and African Pseudhirundo. The African saw-wings (Psalidoprocne) are their likely sister group...
- Ghosh S, Grove A. The Deinococcus radiodurans-encoded HU protein has two DNA-binding domains. Biochemistry. 2006;45:1723-33 pubmed
- McCormack J, Faircloth B, Crawford N, Gowaty P, Brumfield R, Glenn T. Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome Res. 2012;22:746-54 pubmed publisher..One of the most remarkable findings of our study is that ultraconserved elements and their flanking DNA are a rich source of phylogenetic information with strong potential for application across Amniotes. ..