A transcript finishing initiative for closing gaps in the human transcriptome

We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST Clusters, mapped against the genomic sequence. Each pair of EST Clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1% was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted Set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms.

Survival probability of large rapidity gaps in a QCD model with a dynamical infrared mass scale

We compute the survival probability {vertical bar S vertical bar(2)} of large rapidity gaps (LRG) in a QCD based eikonal model with a dynamical gluon mass, where this dynamical infrared mass scale represents the onset of nonperturbative contributions to the diffractive hadron-hadron scattering. Since rapidity gaps can occur in the case of Higgs boson production via fusion of electroweak bosons, we focus on WW -> H fusion processes and show that the resulting {vertical bar S vertical bar(2)} decreases with the increase of the energy of the incoming hadrons; in line with the available experimental data for LRG. We obtain {vertical bar S vertical bar(2)} = 27.6 +/- 7.8% (18.2 +/- 17.0%) at Tevatron (CERN-LHC) energy for a dynamical gluon mass m(g) = 400 MeV. (c) 2006 Elsevier B.V. All rights reserved.

Forward energy flow, central charged-particle multiplicities, and pseudorapidity gaps in W and Z boson events from pp collisions at root s=7 TeV

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Monte Carlo and modified Tanford-Kirkwood results for macromolecular electrostatics calculations

The understanding of electrostatic interactions is an essential aspect of the complex correlation between structure and function of biological macromolecules. It is also important in protein engineering and design. Theoretical studies of such interactions are predominantly done within the framework of Debye-Huckel theory. A classical example is the Tanford-Kirkwood (TK) model. Besides other limitations, this model assumes an infinitesimally small macromolecule concentration. By comparison to Monte Carlo (MC) simulations, it is shown that TK predictions for the shifts in ion binding constants upon addition of salt become less reliable even at moderately macromolecular concentrations. A simple modification based on colloidal literature is suggested to the TK scheme. The modified TK models suggested here satisfactorily predict MC and experimental shifts in the calcium binding constant as a function of protein concentration for the calbindin D-9k mutant and calmodulin.

A critical investigation of the Tanford-Kirkwood scheme by means of Monte Carlo simulations

Monte Carlo simulations are used to assess the adequacy of the Tanford-Kirkwood prescription for electrostatic interactions in macromolecules. Within a continuum dielectric framework, the approach accurately describes salt screening of electrostatic interactions for moderately charged systems consistent with common proteins at physiological conditions. The limitations of the Debye-Huckel theory, which forms the statistical mechanical basis for the Tanford-Kirkwood result, become apparent for highly charged systems. It is shown, both by an analysis of the Debye-Huckel theory and by numerical simulations, that the difference in dielectric permittivity between macromolecule and surrounding solvent does not play a significant role for salt effects if the macromolecule is highly charged. By comparison to experimental data, the continuum dielectric model (combined with either an approximate effective Hamiltonian as in the Tanford-Kirkwood treatment or with exact Monte Carlo simulations) satisfactorily predicts the effects of charge mutation on metal ion binding constants, but only if the macromolecule and solvent are assigned the same or similar permittivities.

Knowledge gaps and bibliographical revision about descriptions of free-swimming anuran larvae from Brazil

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Relaxation-chaos phenomena in celestial mechanics. I. On wisdom's model for the 3/1 kirkwood gap

Sudden eccentricity increases of asteroidal motion in 3/1 resonance with Jupiter were discovered and explained by J. Wisdom through the occurrence of jumps in the action corresponding to the critical angle (resonant combination of the mean motions). We pursue some aspects of this mechanism, which could be termed relaxation-chaos: that is, an unconventional form of homoclinic behavior arising in perturbed integrable Hamiltonian systems for which the KAM theorem hypothesis do not hold. © 1987.

Color evaporation induced rapidity gaps

We show that soft color rearrangement of final states can account for the appearance of rapidity gaps between jets. In the color evaporation model the probability to form a gap is simply determined by the color multiplicity of the final state. This model has no free parameters and reproduces all data obtained by the ZEUS, H1, DØ, and CDF Collaborations. ©1999 The American Physical Society.

Color evaporation induced rapidity gaps

We show that soft color rearrangement of final states can account for the appearance of rapidity gaps between jets. In the color evaporation model the probability to form a gap is simply determined by the color multiplicity of the final state. This model has no free parameters and reproduces all data obtained by the ZEUS, H1, DØ, and CDF collaborations. © 2001 Elsevier Science B.V. All rights reserved.