Genomes and Genes
Experts and Doctors on base sequence in Princeton, Florida, United States
Locale: Princeton, Florida, United States
Topic: base sequence
- Kleinstein S, Singh J. Why are there so few key mutant clones? The influence of stochastic selection and blocking on affinity maturation in the germinal center. Int Immunol. 2003;15:871-84 pubmed..In particular, the blocking model is consistent with the observation that key mutants generally exhibit a higher number of mutations per sequence in the phOx response, but a lower number in the NP response. ..
- Almén M, Lamichhaney S, Berglund J, Grant B, Grant P, Webster M, et al. Adaptive radiation of Darwin's finches revisited using whole genome sequencing. Bioessays. 2016;38:14-20 pubmed publisher..As we review herein, the evolution of such adaptive haplotypes comprising multiple causal changes appears to be an important mechanism contributing to the evolution of biodiversity. ..
- Casciotti K, Ward B. Dissimilatory nitrite reductase genes from autotrophic ammonia-oxidizing bacteria. Appl Environ Microbiol. 2001;67:2213-21 pubmed
- Brinkley P, Class K, Bolen J, Penhallow R. Structure and developmental regulation of the murine ctk gene. Gene. 1995;163:179-84 pubmed..Our results thus show that despite their structural and functional similarities, ctk and csk differ markedly in their patterns of expression. ..
- Lai M, Kirsch D. Nucleotide sequence of cytochrome P450 L1A1 (lanosterol 14 alpha-demethylase) from Candida albicans. Nucleic Acids Res. 1989;17:804 pubmed
- Erginel Unaltuna N, Yang W, Blanar M. Genomic organization and expression of KCNJ8/Kir6.1, a gene encoding a subunit of an ATP-sensitive potassium channel. Gene. 1998;211:71-8 pubmed..Our studies provide information on the complexity of the Kir6.1 transcript in the 5' UTR that may be useful for future investigations on the tissue-specific regulation and function of this KATP channel gene...
- Gebe J, Llewellyn M, Hoggatt H, Aruffo A. Molecular cloning, genomic organization and cell-binding characteristics of mouse Spalpha. Immunology. 2000;99:78-86 pubmed
- Kappes G, Deshpande G, Mulvey B, Horabin J, Schedl P. The Drosophila Myc gene, diminutive, is a positive regulator of the Sex-lethal establishment promoter, Sxl-Pe. Proc Natl Acad Sci U S A. 2011;108:1543-8 pubmed publisher..Here we show that the Drosophila Myc gene diminutive is an X-linked numerator. ..
- Bally Cuif L, Schatz W, Ho R. Characterization of the zebrafish Orb/CPEB-related RNA binding protein and localization of maternal components in the zebrafish oocyte. Mech Dev. 1998;77:31-47 pubmed..We show that this localization is independent of microtubules and microfilaments, and that the distribution of Zorba protein parallels that of its mRNA. ..
- Kinney J, Murugan A, Callan C, Cox E. Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc Natl Acad Sci U S A. 2010;107:9158-63 pubmed publisher..The principles of our method can also be applied to a wide range of other problems in molecular biology. ..
- Jones P, Nawoschik S, Sreekumar K, Uveges A, Tseng E, Zhang L, et al. Tissue distribution and functional analyses of the constitutively active orphan G protein coupled receptors, GPR26 and GPR78. Biochim Biophys Acta. 2007;1770:890-901 pubmed..50) in the so-called DRY box. Site-directed mutants R3.50 in GPR26 were constructed and retained their constitutive activity suggesting that these 2 receptors activate G proteins in a manner that is distinct from other group 1 GPCRs. ..
- Sharma A, Martin M, Okabe J, Truglio R, Dhanjal N, Logan J, et al. An isologous porcine promoter permits high level expression of human hemoglobin in transgenic swine. Biotechnology (N Y). 1994;12:55-9 pubmed..This pig was bred to a non-transgenic animal resulting in the transmission of high level human hemoglobin expression to 5 of 12 progeny. ..
- Clark S, Rose M. Alanine scanning of Arp1 delineates a putative binding site for Jnm1/dynamitin and Nip100/p150Glued. Mol Biol Cell. 2005;16:3999-4012 pubmed..Unlike the actin mutations, none of the ARP1 alleles disrupt filament formation; however, one pointed-end allele delayed the elution of Arp1p on gel filtration, consistent with loss of additional subunits. ..
- Davis G, Srinivasan D, Wittkopp P, Stern D. The function and regulation of Ultrabithorax in the legs of Drosophila melanogaster. Dev Biol. 2007;308:621-31 pubmed..While the enhancer could reside within the small regions we have not surveyed, it is also possible that the enhancer is structurally complex and/or acts only within its native genomic context. ..
- Jabri B, Selby J, Negulescu H, Lee L, Roberts A, Beavis A, et al. TCR specificity dictates CD94/NKG2A expression by human CTL. Immunity. 2002;17:487-99 pubmed..These findings suggest that TCR antigenic specificity dictates NKG2A commitment, which critically regulates subsequent activation of CTL. ..
- Braun M, Silhavy T. Imp/OstA is required for cell envelope biogenesis in Escherichia coli. Mol Microbiol. 2002;45:1289-302 pubmed..Upon depletion of Imp, lipids and outer membrane proteins appear in a novel membrane fraction with higher density than the outer membrane. We propose Imp to be part of a targeting/usher system for components of the outer membrane. ..
- Lazo P, Dorfman K, Noguchi T, Mattei M, Bravo R. Structure and mapping of the fosB gene. FosB downregulates the activity of the fosB promoter. Nucleic Acids Res. 1992;20:343-50 pubmed..We have also shown that FosB and c-Fos can downregulate the activity of the fosB promoter to a similar extent. The fosB gene is located in the [A1-B1] region of mouse chromosome 7. ..
- Katz D, Beer M, Levorse J, Tilghman S. Functional characterization of a novel Ku70/80 pause site at the H19/Igf2 imprinting control region. Mol Cell Biol. 2005;25:3855-63 pubmed..A genome scan revealed that the binding site is found in LINE-1 retrotransposons, suggesting a possible role for Ku70/80 in transposition. ..
- Parks C, Robinson P, Sibille E, Shenk T, Toth M. Increased anxiety of mice lacking the serotonin1A receptor. Proc Natl Acad Sci U S A. 1998;95:10734-9 pubmed..This view is consistent with earlier studies showing that pharmacological activation of the 5-HT system is anxiogenic in animal models and also in humans. ..
- Lamballe F, Tapley P, Barbacid M. trkC encodes multiple neurotrophin-3 receptors with distinct biological properties and substrate specificities. EMBO J. 1993;12:3083-94 pubmed..These observations suggest that the trophic activities of NT-3 in the mammalian nervous system might be mediated by different TrkC receptor isoforms. ..
- Klein R, Parada L, Coulier F, Barbacid M. trkB, a novel tyrosine protein kinase receptor expressed during mouse neural development. EMBO J. 1989;8:3701-9 pubmed..These results suggest that trkB may code for a novel cell surface receptor involved in neurogenesis. ..
- Klages S, Adam D, Class K, Fargnoli J, Bolen J, Penhallow R. Ctk: a protein-tyrosine kinase related to Csk that defines an enzyme family. Proc Natl Acad Sci U S A. 1994;91:2597-601 pubmed..Our results thereby indicate that ctk represents a gene that defines a family of structurally and functionally related Csk-like protein-tyrosine kinases. ..
- Buckbinder L, Talbott R, Seizinger B, Kley N. Gene regulation by temperature-sensitive p53 mutants: identification of p53 response genes. Proc Natl Acad Sci U S A. 1994;91:10640-4 pubmed..These results show that p53 activates the expression of numerous response genes and suggest that multiple effectors may play a role in mediating cellular functions of p53. ..
- Persikov A, Osada R, Singh M. Predicting DNA recognition by Cys2His2 zinc finger proteins. Bioinformatics. 2009;25:22-9 pubmed publisher..An online tool for predicting ZF DNA binding is available at http://compbio.cs.princeton.edu/zf/. ..
- Taylor D, Cheng X, Pawlowski J, Wallace A, Ferrer P, Molloy C. Epiregulin is a potent vascular smooth muscle cell-derived mitogen induced by angiotensin II, endothelin-1, and thrombin. Proc Natl Acad Sci U S A. 1999;96:1633-8 pubmed
- Lahav R, Gammie A, Tavazoie S, Rose M. Role of transcription factor Kar4 in regulating downstream events in the Saccharomyces cerevisiae pheromone response pathway. Mol Cell Biol. 2007;27:818-29 pubmed..Accordingly, we propose that Kar4 plays a critical role in the choreography of the mating response. ..
- Lai M, Bard M, Pierson C, Alexander J, Goebl M, Carter G, et al. The identification of a gene family in the Saccharomyces cerevisiae ergosterol biosynthesis pathway. Gene. 1994;140:41-9 pubmed..Analyses of these genes demonstrated that strains carrying disruptions of sts1+ or YGL022 have ergosterol biosynthesis defects in the enzyme, sterol C-24(28) reductase (Erg4p; encoded by ERG4).(ABSTRACT TRUNCATED AT 250 WORDS) ..
- Jinks T, Calhoun G, Schedl P. Functional conservation of the sex-lethal sex determining promoter, Sxl-Pe, in Drosophila virilis. Dev Genes Evol. 2003;213:155-65 pubmed publisher..These findings suggest that low-affinity target sites for the X/A counting system are critical for the functioning of Sxl-Pe...
- Ko H, Norman R, Tran J, Fuller K, Fukuda M, Eggenschwiler J. Broad-minded links cell cycle-related kinase to cilia assembly and hedgehog signal transduction. Dev Cell. 2010;18:237-47 pubmed publisher..We propose that Bromi and CCRK control the structure of the primary cilium by coordinating assembly of the axoneme and ciliary membrane, allowing Gli proteins to be properly activated in response to Shh signaling. ..
- Landweber L, Pokrovskaya I. Emergence of a dual-catalytic RNA with metal-specific cleavage and ligase activities: the spandrels of RNA evolution. Proc Natl Acad Sci U S A. 1999;96:173-8 pubmed..By breaking apart and joining different RNA strands, such ribozymes could have led to the production of longer and more complex RNA polymers in prebiotic evolution. ..
- Bergsten S, Huang T, Chatterjee S, Gavis E. Recognition and long-range interactions of a minimal nanos RNA localization signal element. Development. 2001;128:427-35 pubmed..Our results suggest that higher order structural interactions within the localization signal, which requires factors such as p75, are necessary for association of nos mRNA with the germ plasm. ..
- Mora T, Walczak A, Bialek W, Callan C. Maximum entropy models for antibody diversity. Proc Natl Acad Sci U S A. 2010;107:5405-10 pubmed publisher..This approach should be applicable to the study of the global properties of other protein families. ..
- Riley T, Yu X, Sontag E, Levine A. The p53HMM algorithm: using profile hidden markov models to detect p53-responsive genes. BMC Bioinformatics. 2009;10:111 pubmed publisher..These methods may also boost performance when applied to other transcription factor binding sites. ..
- Palmer L, Dejori M, Bolanos R, Fasulo D. Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction. BMC Bioinformatics. 2010;11:33 pubmed publisher..Machine learning methods that use comparative and non-comparative features to classify overlaps as true or false can be used to improve the quality of a sequence assembly. ..
- Vazquez Anderson J, Mihailovic M, Baldridge K, Reyes K, Haning K, Cho S, et al. Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions. Nucleic Acids Res. 2017;45:5523-5538 pubmed publisher..Additionally, we demonstrate the applicability of this approach to other bacterial species by predicting sRNA-mRNA binding regions in two newly discovered, though uncharacterized, regulatory RNAs. ..
- Simon H, Oppenheimer S. Advanced mRNA differential display: isolation of a new differentially regulated myosin heavy chain-encoding gene in amphibian limb regeneration. Gene. 1996;172:175-81 pubmed..This differential regulation was confirmed by Northern analysis, and DNA sequencing uncovered a novel newt differentiation-specific transcript encoding a skeletal myosin heavy chain (MHC)...
- Wu J, Ohta N, Zhao J, Newton A. A novel bacterial tyrosine kinase essential for cell division and differentiation. Proc Natl Acad Sci U S A. 1999;96:13068-73 pubmed..DivL is the only reported HPK homologue whose function has been shown to require autophosphorylation on a tyrosine, and, thus, it represents a new class of kinases within this superfamily of protein kinases...
- Cole S, Levorse J, Tilghman S, Vogt T. Clock regulatory elements control cyclic expression of Lunatic fringe during somitogenesis. Dev Cell. 2002;3:75-84 pubmed..A separable Lfng regulatory region directs expression to the prospective rostral aspect of the condensing somite. These independent Lfng regulatory cassettes advance a molecular framework for deciphering somite segmentation. ..
- Xavier K, Bassler B. Regulation of uptake and processing of the quorum-sensing autoinducer AI-2 in Escherichia coli. J Bacteriol. 2005;187:238-48 pubmed..These findings show that, depending on the prevailing growth conditions, the amount of time that the AI-2 signal is present and, in turn, the time that a given community of bacteria remains exposed to this signal can vary greatly. ..
- Fang W, Wang X, Bracht J, Nowacki M, Landweber L. Piwi-interacting RNAs protect DNA against loss during Oxytricha genome rearrangement. Cell. 2012;151:1243-55 pubmed publisher..Our findings highlight small RNAs as powerful transgenerational carriers of epigenetic information for genome programming...
- Weih F, Ryseck R, Chen L, Bravo R. Apoptosis of nur77/N10-transgenic thymocytes involves the Fas/Fas ligand pathway. Proc Natl Acad Sci U S A. 1996;93:5533-8 pubmed..Our results demonstrate that one pathway of apoptosis triggered by Nur77/N10 in double-positive thymocytes occurs through the upregulation of FasL expression resulting in increased signaling through Fas. ..
- Freeman J, Lilley B, Bassler B. A genetic analysis of the functions of LuxN: a two-component hybrid sensor kinase that regulates quorum sensing in Vibrio harveyi. Mol Microbiol. 2000;35:139-49 pubmed..We also show that signalling from the two V. harveyi quorum-sensing systems is not equivalent. AI-1 and LuxN have a much greater effect on the level of LuxO phosphate and therefore Lux expression than do AI-2 and LuxQ. ..
- Szwajkajzer D, Dai L, Fukayama J, Abramczyk B, Fairman R, Carey J. Quantitative analysis of DNA binding by the Escherichia coli arginine repressor. J Mol Biol. 2001;312:949-62 pubmed..The results indicate that subunit assembly plays no role in activation, although communication among subunits of the ArgR hexamer is required for specific DNA binding. The data suggest that DNA is also an allosteric effector of ArgR. ..
- Hunt R, Edris W, Chanda P, Nieuwenhuijsen B, Young K. Snapin interacts with the N-terminus of regulator of G protein signaling 7. Biochem Biophys Res Commun. 2003;303:594-9 pubmed..Our results suggest that RGS7 could play a role in synaptic vesicle exocytosis through its interaction with snapin. ..
- Chang W, Kuo S, Landweber L. A new scrambled gene in the ciliate Uroleptus. Gene. 2006;368:72-7 pubmed..Our findings identify a new scrambled gene in the micronuclear genome of a spirotrichous ciliate, and suggest that even more complicated structures may be present...
- Forrest K, Clark I, Jain R, Gavis E. Temporal complexity within a translational control element in the nanos mRNA. Development. 2004;131:5849-57 pubmed..Thus, independent regulatory modules with temporally distinct activities contribute to spatial regulation of nanos translation. We propose that nanos evolved to exploit two different stage-specific translational regulatory mechanisms. ..
- Tanaka R, Lee L, Schafer B, Kratunis V, Mohler W, Robinson G, et al. Molecular cloning of mevalonate kinase and regulation of its mRNA levels in rat liver. Proc Natl Acad Sci U S A. 1990;87:2872-6 pubmed..These data indicate that long-term regulation of enzyme activity in rat liver is controlled by changes in the levels of mevalonate kinase mRNA. ..
- Sanchez M, Tapley P, Saini S, He B, Pulido D, Barbacid M. Multiple tyrosine protein kinases in rat hippocampal neurons: isolation of Ptk-3, a receptor expressed in proliferative zones of the developing brain. Proc Natl Acad Sci U S A. 1994;91:1819-23 pubmed
- Donovan J, Dufner M, Korennykh A. Structural basis for cytosolic double-stranded RNA surveillance by human oligoadenylate synthetase 1. Proc Natl Acad Sci U S A. 2013;110:1652-7 pubmed publisher..The assembly of this critical active-site structure provides the gate that couples binding of dsRNA to the production and downstream functions of 2-5A. ..
- Murugan A, Mora T, Walczak A, Callan C. Statistical inference of the generation probability of T-cell receptors from sequence repertoires. Proc Natl Acad Sci U S A. 2012;109:16161-6 pubmed publisher..We argue that the use of formal statistical inference methods, of the kind presented in this paper, will be essential for quantitative understanding of the generation and evolution of diversity in the adaptive immune system. ..
- Lenhart K, Lin S, Titus T, Postlethwait J, Burdine R. Two additional midline barriers function with midline lefty1 expression to maintain asymmetric Nodal signaling during left-right axis specification in zebrafish. Development. 2011;138:4405-10 pubmed publisher..Both barriers appear to be conserved across model systems and are thus likely to be present in all vertebrates. ..
- Kobarg J, Schnittger S, Fonatsch C, Lemke H, Bowen M, Buck F, et al. Characterization, mapping and partial cDNA sequence of the 57-kD intracellular Ki-1 antigen. Exp Clin Immunogenet. 1997;14:273-80 pubmed..The Ki-1/57 gene was mapped to the bands 9q22.3-31 of human chromosome 9. This is an area which appears to be associated with secondary chromosomal aberrations in acute myeloid leukemias. ..
- Sandell L, Guan X, Ingram R, Tilghman S. Gatm, a creatine synthesis enzyme, is imprinted in mouse placenta. Proc Natl Acad Sci U S A. 2003;100:4622-7 pubmed..This genomic screen for novel imprinted genes has elucidated a new connection between imprinting and creatine metabolism during embryonic development in mammals...
- Wu J, Ohta N, Newton A. An essential, multicomponent signal transduction pathway required for cell cycle regulation in Caulobacter. Proc Natl Acad Sci U S A. 1998;95:1443-8 pubmed..Our results suggest that an unidentified phosphotransfer protein or kinase (X) is responsible for phosphoryl group transfer to CtrA in the proposed DivJ --> DivK --> X --> CtrA phosphorelay pathway...
- Jones P, Lombardi S, Cockett M. Cloning and tissue distribution of the human G protein beta 5 cDNA. Biochim Biophys Acta. 1998;1402:288-91 pubmed..The clone has a 1059 bp open reading frame and is highly homologous to the murine clone. In contrast to the brain specific mouse beta 5, northern analysis showed it to be expressed in multiple tissues. ..
- Chu C, Cheng D. Expression, purification, characterization of human 3-methylcrotonyl-CoA carboxylase (MCCC). Protein Expr Purif. 2007;53:421-7 pubmed
- Shao Y, Bassler B. Quorum-sensing non-coding small RNAs use unique pairing regions to differentially control mRNA targets. Mol Microbiol. 2012;83:599-611 pubmed publisher..Sequence comparisons reveal that Vibrionaceae species possessing only qrr1 do not have the aphA gene under Qrr sRNA control. Our findings suggest co-evolving relationships between particular Qrr sRNAs and particular mRNA targets. ..
- Landweber L, Kuo T, Curtis E. Evolution and assembly of an extremely scrambled gene. Proc Natl Acad Sci U S A. 2000;97:3298-303 pubmed..We investigate the evolution of this complex gene in three hypotrichous species...
- Duchow H, Brechbiel J, Chatterjee S, Gavis E. The nanos translational control element represses translation in somatic cells by a Bearded box-like motif. Dev Biol. 2005;282:207-17 pubmed..Together, these results suggest that the TCE has appropriated a conserved regulatory motif to expand its function to somatic tissues. ..
- Forman J, Legesse Miller A, Coller H. A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc Natl Acad Sci U S A. 2008;105:14879-84 pubmed publisher..As more genomes are sequenced, the methodological approach that we used for identifying motifs with high sequence conservation will be increasingly valuable for detecting functional sequence motifs within coding regions. ..
- Pirozzi G, Terry R, Epstein D, Labow M. Identification and characterization of a novel surface antigen gene induced in mast cells activated through the high affinity IgE receptor. J Immunol. 1995;155:5811-8 pubmed..Thus, MCA-32 is a novel surface protein whose structure and expression suggest roles in the development and/or activation of mast cells and monocytes. ..
- Paeschke K, McDonald K, Zakian V. Telomeres: structures in need of unwinding. FEBS Lett. 2010;584:3760-72 pubmed publisher..We summarize data showing that perturbation of their telomere activities can lead to telomere dysfunction and genome instability and in some cases human disease. ..
- De Silva E, Gehrke A, Olszewski K, León I, Chahal J, Bulyk M, et al. Specific DNA-binding by apicomplexan AP2 transcription factors. Proc Natl Acad Sci U S A. 2008;105:8393-8 pubmed publisher..Because of their origin in the plant lineage, ApiAP2 proteins have no homologues in the human host and may prove to be ideal antimalarial targets. ..
- Chen S, Foster W, Jure Kunkel M, Girit E, Abraham R, Hefta L, et al. Cloning, expression and characterization of monkey (Macaca fascicularis) CD137. Vet Immunol Immunopathol. 2008;126:377-81 pubmed publisher..Thus, antibodies directed against epitopes in this extracellular domain could have differences in pharmacologic activity between cynomolgus monkeys and human or across individual cynomolgus monkeys. ..