Primary Sequences of Protein-Like Copolymers: Levy Flight Type Long Range Correlations

We consider the statistical properties of primary sequences of two-letter HP copolymers (H for hydrophobic and P for polar) designed to have water soluble globular conformations with H monomers shielded from water inside the shell of P monomers. We show, both by computer simulations and by exact analytical calculation, that for large globules and flexible polymers such sequences exhibit long-range correlations which can be described by Levy-flight statistics.Comment: 4 pages, including 2 figures; several references added, some formulations improve

Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells - a benchmarking study

BACKGROUND: Proteomics research is enabled with the high-throughput technologies, but our ability to identify expressed proteome is limited in small samples. The coverage and consistency of proteome expression are critical problems in proteomics. Here, we propose pathway analysis and combination of microproteomics and transcriptomics analyses to improve mass-spectrometry protein identification from small size samples. RESULTS: Multiple proteomics runs using MCF-7 cell line detected 4,957 expressed proteins. About 80% of expressed proteins were present in MCF-7 transcripts data; highly expressed transcripts are more likely to have expressed proteins. Approximately 1,000 proteins were detected in each run of the small sample proteomics. These proteins were mapped to gene symbols and compared with gene sets representing canonical pathways, more than 4,000 genes were extracted from the enriched gene sets. The identified canonical pathways were largely overlapping between individual runs. Of identified pathways 182 were shared between three individual small sample runs. CONCLUSIONS: Current technologies enable us to directly detect 10% of expressed proteomes from small sample comprising as few as 50 cells. We used knowledge-based approaches to elucidate the missing proteome that can be verified by targeted proteomics. This knowledge-based approach includes pathway analysis and combination of gene expression and protein expression data for target prioritization. Genes present in both the enriched gene sets (canonical pathways collection) and in small sample proteomics data correspond to approximately 50% of expressed proteomes in larger sample proteomics data. In addition, 90% of targets from canonical pathways were estimated to be expressed. The comparison of proteomics and transcriptomics data, suggests that highly expressed transcripts have high probability of protein expression. However, approximately 10% of expressed proteins could not be matched with the expressed transcripts.The cost of this publication was funded by Vladimir Brusic. (Vladimir Brusic)Published versio

Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe

The fission yeast Schizosaccharomyces pombe is a widely used model organism to study basic mechanisms of eukaryotic biology, but unlike other model organisms, its proteome remains largely uncharacterized. Using a shotgun proteomics approach based on multidimensional prefractionation and tandem mass spectrometry, we have detected ∼30% of the theoretical fission yeast proteome. Applying statistical modelling to normalize spectral counts to the number of predicted tryptic peptides, we have performed label-free quantification of 1465 proteins. The fission yeast protein data showed considerable correlations with mRNA levels and with the abundance of orthologous proteins in budding yeast. Functional pathway analysis indicated that the mRNA–protein correlation is strong for proteins involved in signalling and metabolic processes, but increasingly discordant for components of protein complexes, which clustered in groups with similar mRNA–protein ratios. Self-organizing map clustering of large-scale protein and mRNA data from fission and budding yeast revealed coordinate but not always concordant expression of components of functional pathways and protein complexes. This finding reaffirms at the protein level the considerable divergence in gene expression patterns of the two model organisms that was noticed in previous transcriptomic studies

Asymmetry and structural system analysis of the proximal femur meta-epiphysis: osteoarticular anatomical pathology

<p>Abstract</p> <p>Background</p> <p>The human femur is commonly considered as a subsystem of the locomotor apparatus with four conspicuous levels of organization. This phenomenon is the result of the evolution of the locomotor apparatus, which encompasses both constitutional and individual variability. The work therein reported, therefore, underlies the significance of observing anatomical system analysis of the proximal femur meta-epiphysis in normal conditions, according to the anatomic positioning with respect to the right or left side of the body, and the presence of system asymmetry in the meta-epiphysis structure, thus indicating structural and functional asymmetry.</p> <p>Methods</p> <p>A total of 160 femur bones of both sexes were compiled and a morphological study of 15 linear and angulated parameters of proximal femur epiphysis was produced, thus defining the linear/angulated size of tubular bones. The parameters were divided into linear and angulated groups, while maintaining the motion of the hip joint and transmission of stress to the unwanted parts of the limb. Furthermore, the straight and vertical diameters of the femoral head and the length of the femoral neck were also studied. The angle between the neck and diaphysis, the neck antiversion and angle of rotation of the femoral neck were subsequently measured. Finally, the condylo-diaphyseal angle with respect to the axis of extremity was determined. To visualize the force of intersystem ties, we have used the method of correlation galaxy construction.</p> <p>Results</p> <p>The absolute numeral values of each linear parameter were transformed to relative values. The values of superfluity coefficient for each parameter in the right and left femoral bone groups were estimated and Pearson's correlation coefficient has been calculated (> 0.60). Retrospectively, the observed results have confirmed the presence of functional asymmetry in the proximal femur meta-epiphysis. On the basis of compliance or insignificant difference in the confidence interval of the linear parameters, we have revealed, therefore, a discrepancy in values between the neck and the diaphysis angle and the angle of femoral neck rotation (range displacement of confident interval to a greater degree to the right).</p> <p>Conclusion</p> <p>This study assessed the observations of a systemic anatomical study encompassing the proximal femur meta-epiphysis behavior in normal condition. This work has significance in medical practice as the theoretical basis is also required in knowing the decreased frequency and degree of severity of osteoarthritic pathologies in the dominant lower extremity.</p

Is the energy density of the ground state of the sine-Gordon model unbounded from below for beta^2 > 8 pi ?

We discuss Coleman's theorem concerning the energy density of the ground state of the sine-Gordon model proved in Phys. Rev. D 11, 2088 (1975). According to this theorem the energy density of the ground state of the sine-Gordon model should be unbounded from below for coupling constants beta^2 > 8 pi. The consequence of this theorem would be the non-existence of the quantum ground state of the sine-Gordon model for beta^2 > 8 pi. We show that the energy density of the ground state in the sine-Gordon model is bounded from below even for beta^2 > 8 pi. This result is discussed in relation to Coleman's theorem (Comm. Math. Phys. 31, 259 (1973)), particle mass spectra and soliton-soliton scattering in the sine-Gordon model.Comment: 22 pages, Latex, no figures, revised according to the version accepted for publication in Journal of Physics

PCI proteins eIF3e and eIF3m define distinct translation initiation factor 3 complexes

BACKGROUND: PCI/MPN domain protein complexes comprise the 19S proteasome lid, the COP9 signalosome (CSN), and eukaryotic translation initiation factor 3 (eIF3). The eIF3 complex is thought to be composed of essential core subunits required for global protein synthesis and non-essential subunits that may modulate mRNA specificity. Interactions of unclear significance were reported between eIF3 subunits and PCI proteins contained in the CSN. RESULTS: Here, we report the unexpected finding that fission yeast has two distinct eIF3 complexes sharing common core subunits, but distinguished by the PCI proteins eIF3e and the novel eIF3m, which was previously annotated as a putative CSN subunit. Whereas neither eIF3e nor eIF3m contribute to the non-essential activities of CSN in cullin-RING ubiquitin ligase control, eif3m, unlike eif3e, is an essential gene required for global cellular protein synthesis and polysome formation. Using a ribonomic approach, this phenotypic distinction was correlated with a different set of mRNAs associated with the eIF3e and eIF3m complexes. Whereas the eIF3m complex appears to associate with the bulk of cellular mRNAs, the eIF3e complex associates with a far more restricted set. The microarray findings were independently corroborated for a random set of 14 mRNAs by RT-PCR analysis. CONCLUSION: We propose that the PCI proteins eIF3e and eIF3m define distinct eIF3 complexes that may assist in the translation of different sets of mRNAs

PCI proteins eIF3e and eIF3m define distinct translation initiation factor 3 complexes

BACKGROUND: PCI/MPN domain protein complexes comprise the 19S proteasome lid, the COP9 signalosome (CSN), and eukaryotic translation initiation factor 3 (eIF3). The eIF3 complex is thought to be composed of essential core subunits required for global protein synthesis and non-essential subunits that may modulate mRNA specificity. Interactions of unclear significance were reported between eIF3 subunits and PCI proteins contained in the CSN. RESULTS: Here, we report the unexpected finding that fission yeast has two distinct eIF3 complexes sharing common core subunits, but distinguished by the PCI proteins eIF3e and the novel eIF3m, which was previously annotated as a putative CSN subunit. Whereas neither eIF3e nor eIF3m contribute to the non-essential activities of CSN in cullin-RING ubiquitin ligase control, eif3m, unlike eif3e, is an essential gene required for global cellular protein synthesis and polysome formation. Using a ribonomic approach, this phenotypic distinction was correlated with a different set of mRNAs associated with the eIF3e and eIF3m complexes. Whereas the eIF3m complex appears to associate with the bulk of cellular mRNAs, the eIF3e complex associates with a far more restricted set. The microarray findings were independently corroborated for a random set of 14 mRNAs by RT-PCR analysis. CONCLUSION: We propose that the PCI proteins eIF3e and eIF3m define distinct eIF3 complexes that may assist in the translation of different sets of mRNAs

Aerothermodynamic Analysis of a Reentry Brazilian Satellite

This work deals with a computational investigation on the small ballistic reentry Brazilian vehicle SARA (acronyms for SAt\'elite de Reentrada Atmosf\'erica). Hypersonic flows over the vehicle SARA at zero-degree angle of attack in a chemical equilibrium and thermal non-equilibrium are modeled by the Direct Simulation Monte Carlo (DSMC) method, which has become the main technique for studying complex multidimensional rarefied flows, and that properly accounts for the non-equilibrium aspects of the flows. The emphasis of this paper is to examine the behavior of the primary properties during the high altitude portion of SARA reentry. In this way, velocity, density, pressure and temperature field are investigated for altitudes of 100, 95, 90, 85 and 80 km. In addition, comparisons based on geometry are made between axisymmetric and planar two-dimensional configurations. Some significant differences between these configurations were noted on the flowfield structure in the reentry trajectory. The analysis showed that the flow disturbances have different influence on velocity, density, pressure and temperature along the stagnation streamline ahead of the capsule nose. It was found that the stagnation region is a thermally stressed zone. It was also found that the stagnation region is a zone of strong compression, high wall pressure. Wall pressure distributions are compared with those of available experimental data and good agreement is found along the spherical nose for the altitude range investigated.Comment: The paper will be published in Vol. 42 of the Brazilian Journal of Physic

Heavy- to light-meson transition form factors

Semileptonic heavy -> heavy and heavy -> light meson transitions are studied as a phenomenological application of a heavy-quark limit of Dyson-Schwinger equations. Employing two parameters: E, the difference between the mass of the heavy meson and the effective-mass of the heavy quark; and Lambda, the width of the heavy-meson Bethe-Salpeter amplitude, we calculate f_+(t) for all decays on their entire kinematically accessible t-domain. Our study favours f_B in the range 0.135-0.17 GeV and with E=0.44 GeV and 1/Lambda = 0.14 fm we obtain f_+^{B pi}(0) = 0.46. As a result of neglecting 1/m_c-corrections, we estimate that our calculated values of \rho^2 = 0.87 and f_+^{DK}(0)=0.62 are too low by approximately 15%. However, the bulk of these corrections should cancel in our calculated values of Br(D -> \pi l nu)/Br(D -> K l nu)=0.13 and f_+^{D pi}(0)/f_+^{DK}(0) = 1.16.Comment: 26 pages, 3 figures, REVTE

Alternative Methods for Characterization of Extracellular Vesicles

Extracellular vesicles (ECVs) are nano-sized vesicles released by all cells in vitro as well as in vivo. Their role has been implicated mainly in cell–cell communication, but also in disease biomarkers and more recently in gene delivery. They represent a snapshot of the cell status at the moment of release and carry bioreactive macromolecules such as nucleic acids, proteins, and lipids. A major limitation in this emerging new field is the availability/awareness of techniques to isolate and properly characterize ECVs. The lack of gold standards makes comparing different studies very difficult and may potentially hinder some ECVs-specific evidence. Characterization of ECVs has also recently seen many advances with the use of Nanoparticle Tracking Analysis, flow cytometry, cryo-electron microscopy instruments, and proteomic technologies. In this review, we discuss the latest developments in translational technologies involving characterization methods including the facts in their support and the challenges they face