Experts and Doctors on molecular sequence data in Princeton, Florida, United States


Locale: Princeton, Florida, United States
Topic: molecular sequence data

Top Publications

  1. Sharma A, Khoury Christianson A, White S, Dhanjal N, Huang W, Paulhiac C, et al. High-efficiency synthesis of human alpha-endorphin and magainin in the erythrocytes of transgenic mice: a production system for therapeutic peptides. Proc Natl Acad Sci U S A. 1994;91:9337-41 pubmed
    ..Additional applications and potential improvements of this methodology are discussed. ..
  2. Beasley J, McCoy P, Walker T, Dunn D. Miniaturized, ultra-high throughput screening of tyrosine kinases using homogeneous, competitive fluorescence immunoassays. Assay Drug Dev Technol. 2004;2:141-51 pubmed
    ..Additionally, the relative merits of each of these technologies are assessed in terms of assay miniaturization, ease of development, ultimate screening capability, efficiency, and cost. ..
  3. 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. ..
  4. 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...
  5. Pillai R, Marinelli E, Swenson R. A flexible method for preparation of peptide homo- and heterodimers functionalized with affinity probes, chelating ligands, and latent conjugating groups. Biopolymers. 2006;84:576-85 pubmed
    ..Functional molecules are optionally incorporated into the component peptides or into the assembled dimer. The methods are efficient and scaleable. ..
  6. Feng L, Yan H, Wu Z, Yan N, Wang Z, Jeffrey P, et al. Structure of a site-2 protease family intramembrane metalloprotease. Science. 2007;318:1608-12 pubmed publisher
    ..The structure reveals how zinc embedded in an integral membrane protein can catalyze peptide cleavage...
  7. Kuhlman T, Cox E. Site-specific chromosomal integration of large synthetic constructs. Nucleic Acids Res. 2010;38:e92 pubmed publisher
  8. Frankel N, Wang S, Stern D. Conserved regulatory architecture underlies parallel genetic changes and convergent phenotypic evolution. Proc Natl Acad Sci U S A. 2012;109:20975-9 pubmed publisher
    ..Our results suggest that phenotypic convergence resulted from multiple noncoding changes that occurred in parallel in the D. sechellia and D. ezoana lineages. ..
  9. Gresham D, Desai M, Tucker C, Jenq H, Pai D, Ward A, et al. The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet. 2008;4:e1000303 pubmed publisher
    ..Thus, in addition to answering basic mechanistic questions about evolutionary mechanisms, our work suggests that experimental evolution can also shed light on the function and regulation of individual metabolic pathways. ..

More Information

Publications118 found, 100 shown here

  1. Barbacid M, Lamballe F, Pulido D, Klein R. The trk family of tyrosine protein kinase receptors. Biochim Biophys Acta. 1991;1072:115-27 pubmed
  2. Emanuel S, Engle L, Chao G, Zhu R, Cao C, Lin Z, et al. A fibronectin scaffold approach to bispecific inhibitors of epidermal growth factor receptor and insulin-like growth factor-I receptor. MAbs. 2011;3:38-48 pubmed
    ..Our results illustrate a technological advancement for constructing multi-specific biologics in cancer therapy. ..
  3. Pausch M, Lai M, Tseng E, Paulsen J, Bates B, Kwak S. Functional expression of human and mouse P2Y12 receptors in Saccharomyces cerevisiae. Biochem Biophys Res Commun. 2004;324:171-7 pubmed
    ..Murine P2Y12 mRNA was expressed at high levels in the brain and at lower levels in a variety of peripheral tissues. In situ hybridization analysis indicated glia-specific expression within the brain. ..
  4. 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. ..
  5. 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. ..
  6. 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...
  7. 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
  8. Wu J, Tolstykh T, Lee J, Boyd K, Stock J, Broach J. Carboxyl methylation of the phosphoprotein phosphatase 2A catalytic subunit promotes its functional association with regulatory subunits in vivo. EMBO J. 2000;19:5672-81 pubmed
    ..These phenotypes can be reversed by overexpression of the B regulatory subunit. These results demonstrate that Ppm1 is the sole PP2A methyltransferase in yeast and that its activity is required for the integrity of the PP2A holoenzyme. ..
  9. 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...
  10. 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. ..
  11. Farley E, Olson K, Zhang W, Rokhsar D, Levine M. Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers. Proc Natl Acad Sci U S A. 2016;113:6508-13 pubmed publisher
    ..As a result, enhancers with low binding affinities but optimal syntax may be a vastly underappreciated feature of the regulatory genome. ..
  12. 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...
  13. Adhitya A, Thomas F, Ward B. Diversity of assimilatory nitrate reductase genes from plankton and epiphytes associated with a seagrass bed. Microb Ecol. 2007;54:587-97 pubmed
  14. McGinn P, Morel F. Expression and regulation of carbonic anhydrases in the marine diatom Thalassiosira pseudonana and in natural phytoplankton assemblages from Great Bay, New Jersey. Physiol Plant. 2008;133:78-91 pubmed publisher
  15. Roongta U, Pabalan J, Wang X, Ryseck R, Fargnoli J, Henley B, et al. Cancer cell dependence on unsaturated fatty acids implicates stearoyl-CoA desaturase as a target for cancer therapy. Mol Cancer Res. 2011;9:1551-61 pubmed publisher
    ..Altogether, these results suggest that desaturated fatty acids are required for tumor cell survival and that SCD may represent a viable target for the development of novel agents for cancer therapy. ..
  16. Manne V, Roberts D, Tobin A, O ROURKE E, de Virgilio M, Meyers C, et al. Identification and preliminary characterization of protein-cysteine farnesyltransferase. Proc Natl Acad Sci U S A. 1990;87:7541-5 pubmed
    ..Availability of an in vitro protein farnesyltransferase assay should be useful in screening for potential inhibitors of ras oncogene function that will not interfere with other aspects of the mevalonate pathway. ..
  17. Samuels M, Deshpande G, Schedl P. Activities of the Sex-lethal protein in RNA binding and protein:protein interactions. Nucleic Acids Res. 1998;26:2625-37 pubmed
    ..Finally, we show that the interaction of Sxl with the snRNP protein Snf is mediated by the R1 RRM domain. ..
  18. Naureckiene S, Ma L, Sreekumar K, Purandare U, Lo C, Huang Y, et al. Functional characterization of Narc 1, a novel proteinase related to proteinase K. Arch Biochem Biophys. 2003;420:55-67 pubmed
  19. Feng L, Gell D, Zhou S, Gu L, Kong Y, Li J, et al. Molecular mechanism of AHSP-mediated stabilization of alpha-hemoglobin. Cell. 2004;119:629-40 pubmed
    ..These observations reveal the molecular mechanisms by which AHSP stabilizes free alphaHb. ..
  20. 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. ..
  21. Betty M, Harnish S, Rhodes K, Cockett M. Distribution of heterotrimeric G-protein beta and gamma subunits in the rat brain. Neuroscience. 1998;85:475-86 pubmed
    ..The localizations of the G-protein beta and gamma subunits, and their potential coupling to various receptor/effector systems, are discussed. ..
  22. Smith G, Enquist L. A self-recombining bacterial artificial chromosome and its application for analysis of herpesvirus pathogenesis. Proc Natl Acad Sci U S A. 2000;97:4873-8 pubmed
    ..Recombination is efficient, and pure virus lacking the BAC vector backbone is immediately isolated from transfected mammalian cells without the need of serial passage or plaque purification. ..
  23. Onstott T, Moser D, Pfiffner S, Fredrickson J, Brockman F, Phelps T, et al. Indigenous and contaminant microbes in ultradeep mines. Environ Microbiol. 2003;5:1168-91 pubmed
    ..Pore water and rock geochemical analyses suggest that these SRB's may have been sustained by sulphate diffusing from the adjacent U-rich, Carbon Leader where it was formed by radiolysis of sulphide. ..
  24. Furlong M, Zhao S, Mylott W, Jenkins R, Gao M, Hegde V, et al. Dual universal peptide approach to bioanalysis of human monoclonal antibody protein drug candidates in animal studies. Bioanalysis. 2013;5:1363-76 pubmed publisher
    ..Improvements reported herein to the universal peptide assay will enable more reliable quantification of human monoclonal antibody protein drug candidates in animal studies. ..
  25. Queenan A, Barcelo G, Van Buskirk C, Schupbach T. The transmembrane region of Gurken is not required for biological activity, but is necessary for transport to the oocyte membrane in Drosophila. Mech Dev. 1999;89:35-42 pubmed
    ..We conclude that secretion of Gurken requires its transmembrane region, and propose a model in which the gene cornichon mediates this process. ..
  26. Mancini Dinardo D, Steele S, Ingram R, Tilghman S. A differentially methylated region within the gene Kcnq1 functions as an imprinted promoter and silencer. Hum Mol Genet. 2003;12:283-94 pubmed
    ..We propose, on the basis of these findings, that the Kcnq1 ICR functions as a silencer on the paternal chromosome to effect the repression of neighboring genes. ..
  27. 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. ..
  28. 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. ..
  29. 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. ..
  30. Perez Villar J, O Day K, Hewgill D, Nadler S, Kanner S. Nuclear localization of the tyrosine kinase Itk and interaction of its SH3 domain with karyopherin alpha (Rch1alpha). Int Immunol. 2001;13:1265-74 pubmed
    ..Further, nuclear localization of Itk and TCR-CD3-mediated IL-2 production were significantly down-regulated following expression of the Rch1alpha-P242A mutant, implicating a role for Rch1alpha in the nuclear translocation of Itk. ..
  31. Ramamurthy V, Krystek S, Bush A, Wei A, Emanuel S, Das Gupta R, et al. Structures of adnectin/protein complexes reveal an expanded binding footprint. Structure. 2012;20:259-69 pubmed publisher
    ..Alanine-scanning mutagenesis confirmed the calculated binding energies of these ? strand interactions, indicating that these nonloop residues can expand the available binding footprint. ..
  32. 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. ..
  33. Krystek S, Dias J. Glycoprotein hormones tied but not tethered like other cysteine-knot cytokines. Trends Pharmacol Sci. 2005;26:439-42 pubmed
  34. Rosa J, Casaroli Marano R, Buckler A, Vilaro S, Barbacid M. p619, a giant protein related to the chromosome condensation regulator RCC1, stimulates guanine nucleotide exchange on ARF1 and Rab proteins. EMBO J. 1996;15:4262-73 pubmed
    ..These observations suggest that p619 is a Brefeldin A-sensitive Golgi protein that functions as a guanine nucleotide exchange factor for ARF1 and, possibly, for members of the Rab family of proteins. ..
  35. Wu G, Chen Y, Ozdamar B, Gyuricza C, Chong P, Wrana J, et al. Structural basis of Smad2 recognition by the Smad anchor for receptor activation. Science. 2000;287:92-7 pubmed
    ..Comparison of the structures between Smad2 and a comediator Smad suggests a model for how receptor-regulated Smads are recognized by the type I receptors. ..
  36. 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. ..
  37. Hulmes J, Corbett M, Zysk J, Bohlen P, Eppler C. Partial amino acid sequence of a somatostatin receptor isolated from GH4C1 pituitary cells. Biochem Biophys Res Commun. 1992;184:131-6 pubmed
    ..1992) Proc. Natl. Acad. Sci. U.S.A. 89, 251-255] except for a single valine to isoleucine substitution. This is the first report of amino acid sequence from a purified somatostatin receptor. ..
  38. Kish K, McDonnell P, Goldfarb V, Gao M, Metzler W, Langley D, et al. Cloning, purification, crystallization and preliminary X-ray analysis of the catalytic domain of human receptor-like protein tyrosine phosphatase γ in three different crystal forms. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011;67:768-74 pubmed publisher
    ..An orthorhombic crystal form and a trigonal crystal form were obtained both with and without ligand, and a monoclinic crystal form was only obtained in the presence of a particularly elaborated inhibitor. ..
  39. Bally Cuif L, Dubois L, Vincent A. Molecular cloning of Zcoe2, the zebrafish homolog of Xenopus Xcoe2 and mouse EBF-2, and its expression during primary neurogenesis. Mech Dev. 1998;77:85-90 pubmed
    ..At later stages, Zcoe2 is expressed in early forming neurons of the anterior brain and is a marker of the olfactory placodes. ..
  40. Swan A, Barcelo G, Schupbach T. Drosophila Cks30A interacts with Cdk1 to target Cyclin A for destruction in the female germline. Development. 2005;132:3669-78 pubmed
    ..We also find that a second closely related Cks gene, Cks85A, plays a distinct, non-overlapping role in Drosophila, and the two genes cannot functionally replace each other. ..
  41. Pane A, Wehr K, Schupbach T. zucchini and squash encode two putative nucleases required for rasiRNA production in the Drosophila germline. Dev Cell. 2007;12:851-62 pubmed
    ..We show that these defects are due to the inability of zuc and squ mutants to produce repeat-associated small interfering RNAs. ..
  42. Fach E, Garulacan L, Gao J, Xiao Q, Storm S, Dubaquie Y, et al. In vitro biomarker discovery for atherosclerosis by proteomics. Mol Cell Proteomics. 2004;3:1200-10 pubmed
  43. Melvin I, Weston J, Leslie C, Noble W. Combining classifiers for improved classification of proteins from sequence or structure. BMC Bioinformatics. 2008;9:389 pubmed publisher
    ..Code and data sets are available at ..
  44. Sun Y, Yan Y, Denef N, Schupbach T. Regulation of somatic myosin activity by protein phosphatase 1? controls Drosophila oocyte polarization. Development. 2011;138:1991-2001 pubmed publisher
    ..Interestingly, our results also demonstrate a role of PP1? in generating the polarizing signal independently of Notch, indicating a direct involvement of somatic myosin activity in axis formation. ..
  45. Phillips R, Ernst R, Brunk B, Ivanova N, Mahan M, Deanehan J, et al. The genetic program of hematopoietic stem cells. Science. 2000;288:1635-40 pubmed
    ..The complete data, available in a biological process-oriented database, represent the molecular phenotype of the hematopoietic stem cell. ..
  46. Casciotti K, Ward B. Phylogenetic analysis of nitric oxide reductase gene homologues from aerobic ammonia-oxidizing bacteria. FEMS Microbiol Ecol. 2005;52:197-205 pubmed
    ..These results expand the database of norB homologue sequences in nitrifying bacteria. ..
  47. Han Y, Whitney G, Donovan J, Korennykh A. Innate immune messenger 2-5A tethers human RNase L into active high-order complexes. Cell Rep. 2012;2:902-13 pubmed publisher
    ..These data reveal a function for the ANK domain as a 2-5A-sensing homo-oligomerization device and describe a nonlinear, ultrasensitive regulation in the 2-5A/RNase L system poised for amplification of the IFN response. ..
  48. Constantine K, Mueller L, Goldfarb V, Wittekind M, Metzler W, Yanchunas J, et al. Characterization of NADP+ binding to perdeuterated MurB: backbone atom NMR assignments and chemical-shift changes. J Mol Biol. 1997;267:1223-46 pubmed
    ..Overall, our results are consistent with MurB having a flexible active site. ..
  49. Wu J, Hu M, Chai J, Seoane J, Huse M, Li C, et al. Crystal structure of a phosphorylated Smad2. Recognition of phosphoserine by the MH2 domain and insights on Smad function in TGF-beta signaling. Mol Cell. 2001;8:1277-89 pubmed
    ..These observations define a bifunctional role for the MH2 domain as a pSer-X-pSer binding module in receptor Ser/Thr kinase signaling pathways. ..
  50. Miller S, Xavier K, Campagna S, Taga M, Semmelhack M, Bassler B, et al. Salmonella typhimurium recognizes a chemically distinct form of the bacterial quorum-sensing signal AI-2. Mol Cell. 2004;15:677-87 pubmed publisher
  51. Zhu H, Cong J, Shenk T. Use of differential display analysis to assess the effect of human cytomegalovirus infection on the accumulation of cellular RNAs: induction of interferon-responsive RNAs. Proc Natl Acad Sci U S A. 1997;94:13985-90 pubmed
    ..These RNAs accumulate after infection with virus that has been inactivated by treatment with UV light, indicating that the inducer is present in virions. We conclude that human cytomegalovirus induces interferon-responsive mRNAs. ..
  52. Swem L, Swem D, Wingreen N, Bassler B. Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi. Cell. 2008;134:461-73 pubmed publisher
    ..We find that quorum-sensing-mediated communication can be manipulated positively and negatively to control bacterial behavior and, more broadly, that signaling parameters can be deduced from in vivo data. ..
  53. Lyman M, Kemp C, Taylor M, Enquist L. Comparison of the pseudorabies virus Us9 protein with homologs from other veterinary and human alphaherpesviruses. J Virol. 2009;83:6978-86 pubmed publisher
    ..EHV-1 and BHV-1 Us9 were able to fully compensate for the loss of PRV Us9, whereas VZV and HSV-1 Us9 proteins were unable to functionally replace PRV Us9 when they were expressed in a PRV background...
  54. Young N, DiMaggio P, Garcia B. The significance, development and progress of high-throughput combinatorial histone code analysis. Cell Mol Life Sci. 2010;67:3983-4000 pubmed publisher
    ..Recently, progress has been made in determining such information quickly, quantitatively and sensitively. Here we review both the historical and recent progress toward routine and rapid combinatorial histone code analysis. ..
  55. Zhen Y, Aardema M, Medina E, Schumer M, Andolfatto P. Parallel molecular evolution in an herbivore community. Science. 2012;337:1634-7 pubmed
    ..Together, these findings support the hypothesis that adaptation tends to take evolutionary paths that minimize negative pleiotropy. ..
  56. 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. ..
  57. Ahn D, Ruvinsky I, Oates A, Silver L, Ho R. tbx20, a new vertebrate T-box gene expressed in the cranial motor neurons and developing cardiovascular structures in zebrafish. Mech Dev. 2000;95:253-8 pubmed
    ..During development, tbx20 is expressed in embryonic structures of both mesodermal and ectodermal origins, including the heart, cranial motor neurons, and the roof of the dorsal aorta. ..
  58. Ha S, Gross B, Walker S. E. Coli MurG: a paradigm for a superfamily of glycosyltransferases. Curr Drug Targets Infect Disord. 2001;1:201-13 pubmed
    ..A better understanding of MurG could lead to the development of new drugs to combat antibiotic resistant infections, and may also shed light on a broad class of glycosyltransferases. ..
  59. Tibbetts M, Shiozaki E, Gu L, McDonald E, El Deiry W, Shi Y. Crystal structure of a FYVE-type zinc finger domain from the caspase regulator CARP2. Structure. 2004;12:2257-63 pubmed
    ..Structural analyses provide insights into the possible function of this unique subfamily of FYVE-type domains. ..
  60. 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. ..
  61. 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. ..
  62. 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) ..
  63. 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
  64. Wu J, Cocina A, Chai J, Hay B, Shi Y. Structural analysis of a functional DIAP1 fragment bound to grim and hid peptides. Mol Cell. 2001;8:95-104 pubmed
    ..Our study reveals the structural conservation and diversity necessary for the binding of IAPs by the Drosophila Hid/Grim/Reaper and the mammalian Smac proteins. ..
  65. Wang B, Zhao A, Novick R, Muir T. Activation and inhibition of the receptor histidine kinase AgrC occurs through opposite helical transduction motions. Mol Cell. 2014;53:929-40 pubmed publisher
    ..Binding of agonist or inverse-agonist peptides results in twisting of the linker in different directions. These two observations provide a view of the molecular motions triggered by ligand binding in an intact membrane-bound RHK. ..
  66. Buckbinder L, Velasco Miguel S, Chen Y, Xu N, Talbott R, Gelbert L, et al. The p53 tumor suppressor targets a novel regulator of G protein signaling. Proc Natl Acad Sci U S A. 1997;94:7868-72 pubmed
    ..Thus, through the induction of A28-RGS14, p53 may regulate cellular sensitivity to growth and/or survival factors acting through G protein-coupled receptor pathways. ..
  67. Chai J, Shiozaki E, Srinivasula S, Wu Q, Datta P, Alnemri E, et al. Structural basis of caspase-7 inhibition by XIAP. Cell. 2001;104:769-80 pubmed
    ..Our biochemical and structural analyses reveal that the BIR domains are dispensable for the inhibition of caspase-3 and -7. This study provides a structural basis for the design of the next-generation caspase inhibitors. ..
  68. 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...
  69. Gupta T, Schupbach T. Cct1, a phosphatidylcholine biosynthesis enzyme, is required for Drosophila oogenesis and ovarian morphogenesis. Development. 2003;130:6075-87 pubmed
    ..These data provide the first evidence for a specific role for CCT, and thus for phosphatidylcholine, in patterning during development. ..
  70. Lenz D, Mok K, Lilley B, Kulkarni R, Wingreen N, Bassler B. The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell. 2004;118:69-82 pubmed publisher
    ..We propose that Hfq, together with these sRNAs, creates an ultrasensitive regulatory switch that controls the critical transition into the high cell density, quorum-sensing mode...
  71. 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. ..
  72. Yang W, Levesque P, Little W, Conder M, Shalaby F, Blanar M. KvLQT1, a voltage-gated potassium channel responsible for human cardiac arrhythmias. Proc Natl Acad Sci U S A. 1997;94:4017-21 pubmed
    ..Coexpression of minK with KvLQT1 results in a conductance with pharmacological and biophysical properties more similar to I(Ks) than other known delayed rectifier K+ currents in the heart. ..
  73. Nodelman I, Bowman G, Lindberg U, Schutt C. X-ray structure determination of human profilin II: A comparative structural analysis of human profilins. J Mol Biol. 1999;294:1271-85 pubmed
    ..These observations are important for the understanding of the functional and structural differences between these two classes of profilin isoforms. ..
  74. Shen S, Tobery C, Rose M. Prm3p is a pheromone-induced peripheral nuclear envelope protein required for yeast nuclear fusion. Mol Biol Cell. 2009;20:2438-50 pubmed publisher
    ..Genetic analysis, colocalization, and biochemical experiments indicate that Prm3p interacts directly with Kar5p, suggesting that nuclear membrane fusion is mediated by a protein complex. ..
  75. 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. ..
  76. 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. ..
  77. Ivanovska I, Rose M. Fine structure analysis of the yeast centrin, Cdc31p, identifies residues specific for cell morphology and spindle pole body duplication. Genetics. 2001;157:503-18 pubmed
    ..Mutations in the C-terminal region were also defective for interaction with Kic1p. Mapping the alleles onto a predicted structure of Cdc31p, we have identified surfaces likely to be important for interacting with both Kar1p and Kic1p. ..
  78. Van Buskirk C, Schupbach T. Half pint regulates alternative splice site selection in Drosophila. Dev Cell. 2002;2:343-53 pubmed
    ..In particular, hfp mutants display striking defects in the developmentally regulated splicing of ovarian tumor (otu). Furthermore, transgenic expression of the missing otu splice form can rescue the ovarian phenotypes of hfp. ..
  79. 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. ..
  80. Wu J, Krawitz A, Chai J, Li W, Zhang F, Luo K, et al. Structural mechanism of Smad4 recognition by the nuclear oncoprotein Ski: insights on Ski-mediated repression of TGF-beta signaling. Cell. 2002;111:357-67 pubmed
    ..Intriguingly, the structure of the Ski fragment, stabilized by a bound zinc atom, resembles the SAND domain, in which the corresponding I loop is responsible for DNA binding. ..
  81. Nowacki M, Higgins B, Maquilan G, Swart E, Doak T, Landweber L. A functional role for transposases in a large eukaryotic genome. Science. 2009;324:935-8 pubmed publisher
    ..This study suggests a new important role in Oxytricha for this large portion of genomic DNA that was previously thought of as junk...
  82. Kotnis S, Bingham B, Vasilyev D, Miller S, Bai Y, Yeola S, et al. Genetic and functional analysis of human P2X5 reveals a distinct pattern of exon 10 polymorphism with predominant expression of the nonfunctional receptor isoform. Mol Pharmacol. 2010;77:953-60 pubmed publisher
  83. 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. ..
  84. 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. ..
  85. Surrey T, Elowitz M, Wolf P, Yang F, Nedelec F, Shokat K, et al. Chromophore-assisted light inactivation and self-organization of microtubules and motors. Proc Natl Acad Sci U S A. 1998;95:4293-8 pubmed
    ..In this system, CALI can effectively perturb local structure formation by blocking or reducing the degree of aster formation in chosen regions of the sample, without influencing structure formation elsewhere. ..
  86. Hu Y, Chen L, Ha S, Gross B, Falcone B, Walker D, et al. Crystal structure of the MurG:UDP-GlcNAc complex reveals common structural principles of a superfamily of glycosyltransferases. Proc Natl Acad Sci U S A. 2003;100:845-9 pubmed
  87. 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. ..
  88. 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. ..
  89. 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. ..
  90. Shiozaki E, Gu L, Yan N, Shi Y. Structure of the BRCT repeats of BRCA1 bound to a BACH1 phosphopeptide: implications for signaling. Mol Cell. 2004;14:405-12 pubmed
    ..Additional structural analysis revealed significant implications for understanding the function of the BRCT family of proteins in DNA damage and repair signaling. ..
  91. McFarland C, Chang W, Kuo S, Landweber L. Conserved linkage of two genes on the same macronuclear chromosome in spirotrichous ciliates. Chromosoma. 2006;115:129-38 pubmed
    ..This study is the first to examine gene linkage in the macronucleus of several spirotrichs and may provide insight into the evolution of multi-gene macronuclear chromosomes and chromosomal fragmentation in spirotrichs...
  92. Melvin I, Ie E, Kuang R, Weston J, Stafford W, Leslie C. SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition. BMC Bioinformatics. 2007;8 Suppl 4:S2 pubmed
    ..By combining state-of-the-art SVM kernel methods with a novel multi-class algorithm, the SVM-Fold system delivers efficient and accurate protein fold and superfamily recognition. ..