Proteomic analysis of the bacterial cell cycle

A global approach was used to analyze protein synthesis and stability during the cell cycle of the bacterium Caulobacter crescentus. Approximately one-fourth (979) of the estimated C. crescentus gene products were detected by two-dimensional gel electrophoresis, 144 of which showed differential cell cycle expression patterns. Eighty-one of these proteins were identified by mass spectrometry and were assigned to a wide variety of functional groups. Pattern analysis revealed that coexpression groups were functionally clustered. A total of 48 proteins were rapidly degraded in the course of one cell cycle. More than half of these unstable proteins were also found to be synthesized in a cell cycle-dependent manner, establishing a strong correlation between rapid protein turnover and the periodicity of the bacterial cell cycle. This is, to our knowledge, the first evidence for a global role of proteolysis in bacterial cell cycle control.

Novel phenomena in dilute electron systems in two dimensions

For the past two decades, all two-dimensional systems of electrons were believed to be insulating in the limit of zero temperature. Recent experiments provide evidence for an unexpected transition to a conducting phase at very low electron densities. The nature of this phase is not understood and is currently the focus of intense theoretical and experimental attention.

Faithful representation of similarities among three-dimensional shapes in human vision.

Efficient and reliable classification of visual stimuli requires that their representations reside a low-dimensional and, therefore, computationally manageable feature space. We investigated the ability of the human visual system to derive such representations from the sensory input-a highly nontrivial task, given the million or so dimensions of the visual signal at its entry point to the cortex. In a series of experiments, subjects were presented with sets of parametrically defined shapes; the points in the common high-dimensional parameter space corresponding to the individual shapes formed regular planar (two-dimensional) patterns such as a triangle, a square, etc. We then used multidimensional scaling to arrange the shapes in planar configurations, dictated by their experimentally determined perceived similarities. The resulting configurations closely resembled the original arrangements of the stimuli in the parameter space. This achievement of the human visual system was replicated by a computational model derived from a theory of object representation in the brain, according to which similarities between objects, and not the geometry of each object, need to be faithfully represented.

Projection structure of frog rhodopsin in two crystal forms.

Rhodopsin is the G protein-coupled receptor that upon light activation triggers the visual transduction cascade. Rod cell outer segment disc membranes were isolated from dark-adapted frog retinas and were extracted with Tween detergents to obtain two-dimensional rhodopsin crystals for electron crystallography. When Tween 80 was used, tubular structures with a p2 lattice (a = 32 A, b = 83 A, gamma = 91 degrees) were formed. The use of a Tween 80/Tween 20 mixture favored the formation of larger p22(1)2(1) lattices (a = 40 A, b = 146 A, gamma = 90 degrees). Micrographs from frozen hydrated frog rhodopsin crystals were processed, and projection structures to 7-A resolution for the p22(1)2(1) form and to 6-A resolution for the p2 form were calculated. The maps of frog rhodopsin in both crystal forms are very similar to the 9-A map obtained previously for bovine rhodopsin and show that the arrangement of the helices is the same. In a tentative topographic model, helices 4, 6, and 7 are nearly perpendicular to the plane of the membrane. In the higher-resolution projection maps of frog rhodopsin, helix 5 looks more tilted than it appeared previously. The quality of the two frog rhodopsin crystals suggests that they would be suitable to obtain a three-dimensional structure in which all helices would be resolved.

Estudo ecocardiográfico da função ventricular esquerda em pacientes com lúpus eritematoso sistêmico juvenil através da técnica de Speckle-Tracking bidimensional

Objetivo: O principal propósito do estudo foi pesquisar a disfunção ventricular esquerda subclínica em pacientes com lúpus eritematoso sistêmico juvenil (LESJ) através da técnica de speckle-tracking bidimensional. Foi investigada ainda uma possível correlação entre o comprometimento da deformação miocárdica e o SLEDAI-2K (Systemic Lupus Erithematosus Disease Activity Index 2000), bem como a presença de fatores de risco cardiovascular, tanto tradicionais como ligados à doença. Métodos: 50 pacientes assintomáticos do ponto de vista cardiovascular e 50 controles saudáveis (14,74 vs. 14,82 anos, p=0.83) foram avaliados pelo ecocardiograma convencional e pelo speckle-tracking bidimensional. Resultados: Apesar da fração de ejeção normal, os pacientes apresentaram redução de todos os parâmetros de deformação miocárdica longitudinal e radial, quando comparados aos controles: strain de pico sistólico longitudinal [-20,3 (-11 a -26) vs. -22 (-17,8 a -30.4) %, p < 0,0001], strain rate de pico sistólico longitudinal [-1,19 ± 0,21 vs. -1,3 ± 0,25 s-1, p=0,0005], strain rate longitudinal na diástole precoce [1,7 (0,99 a 2,95) vs. 2 (1,08 a 3,00) s-1 , p=0,0034], strain de pico sistólico radial [33,09 ± 8,6 vs. 44,36 ± 8,72%, p < 0,0001], strain rate de pico sistólico radial [1,98 ± 0,53 vs. 2,49 ± 0,68 s-1, p < 0,0001] e strain rate radial na diástole precoce [-2,31 ± 0,88 vs. -2,75 ± 0,97 s-1, p=0,02]. O strain de pico sistólico circunferencial [-23,67 ± 3,46 vs. - 24,6 ± 2,86%, p=0,43] e o strain rate circunferencial na diástole precoce [2 (0,88 a 3,4) vs. 1,99 (1,19 a 3,7) s-1, p=0,88] foram semelhantes em pacientes e controles. Apenas o strain rate de pico sistólico circunferencial [-1,5 ± 0,3 vs. -1,6 ± 0,3 s-1, p=0,036] mostrou-se reduzido no LESJ. Uma correlação negativa foi identificada entre o strain de pico sistólico longitudinal e o SLEDAI-2K (r = - 0,52; p < 0,0001) e também o número de fatores de risco cardiovascular por paciente (r = -0,32, p=0,024). Conclusões: Foi evidenciada disfunção sistólica e diastólica subclínica de ventrículo esquerdo no LESJ através da técnica de speckle-tracking bidimensional. A atividade da doença e a exposição aos fatores de risco cardiovascular provavelmente contribuíram para o comprometimento da deformação miocárdica nesses pacientes

Comparative proteomic analysis of GS-NSO murine myeloma cell lines with varying recombinant monoclonal antibody production rate

We have employed an inverse engineering strategy based on quantitative proteome analysis to identify changes in intracellular protein abundance that correlate with increased specific recombinant monoclonal antibody production (qMab) by engineered murine myeloma (NSO) cells. Four homogeneous NSO cell lines differing in qMab were isolated from a pool of primary transfectants. The proteome of each stably transfected cell line was analyzed at mid-exponential growth phase by two-dimensional gel electrophoresis (2D-PAGE) and individual protein spot volume data derived from digitized gel images were compared statistically. To identify changes in protein abundance associated with qMab clatasets were screened for proteins that exhibited either a linear correlation with cell line qMab or a conserved change in abundance specific only to the cell line with highest qMab. Several proteins with altered abundance were identified by mass spectrometry. Proteins exhibiting a significant increase in abundance with increasing qMab included molecular chaperones known to interact directly with nascent immunoglobulins during their folding and assembly (e.g., BiP, endoplasmin, protein disulfide isomerase). 2D-PAGE analysis showed that in all cell lines Mab light chain was more abundant than heavy chain, indicating that this is a likely prerequisite for efficient Mab production. In summary, these data reveal both the adaptive responses and molecular mechanisms enabling mammalian cells in culture to achieve high-level recombinant monoclonal antibody production. (C) 2004 Wiley Periodicals, Inc.

Numerical evaluation of three dimensional effects in planar flow birefringence

The influence of three dimensional effects on isochromatic birefringence is evaluated for planar flows by means of numerical simulation. Two fluid models are investigated in channel and abrupt contraction geometries. In practice, the flows are confined by viewing windows, which alter the stresses along the optical path. The observed optical properties differ therefore from their counterpart in an ideal two-dimensional flow. To investigate the influence of these effects, the stress optical rule and the differential propagation Mueller matrix are used. The material parameters are selected so that a retardation of multiple orders is achieved, as is typical for highly birefringent melts. Errors due to three dimensional effects are mainly found on the symmetry plane, and increase significantly with the flow rate. Increasing the geometric aspect ratio improve the accuracy provided that the error on the retardation is less than one order. (C) 2004 Elsevier B.V. All rights reserved.

Three-dimensional simulation of the rolling of a saturated fibro-porous media

This paper describes recent advances made in computational modelling of the sugar cane liquid extraction process. The saturated fibro-porous material is rolled between circumferentially grooved rolls, which enhance frictional grip and provide a low-resistance path for liquid flow during the extraction process. Previously reported two-dimensional (2D) computational models, account for the large deformation of the porous material by solving the fully coupled governing fibre stress and fluid-flow equations using finite element techniques. While the 2D simulations provide much insight into the overarching cause-effect relationships, predictions of mechanical quantities such as roll separating force and particularly torque as a function of roll speed and degree of compression are not satisfactory for industrial use. It is considered that the unsatisfactory response in roll torque prediction may be due to the stress levels that exist between the groove tips and roots which have been largely neglected in the geometrically simplified 2D model. This paper gives results for both two- and three-dimensional finite element models and highlights their strengths and weaknesses in predicting key milling parameters. (c) 2005 Elsevier B.V. All rights reserved.

Isolation and characterization of novel cyclotides from Viola hederaceae - Solution structure and anti-HIV activity of vhl-1, a leaf-specific expressed cyclotide

Based on a newly established sequencing strategy featured by its efficiency, simplicity, and easy manipulation, the sequences of four novel cyclotides (macrocyclic knotted proteins) isolated from an Australian plant Viola hederaceae were determined. The three-dimensional solution structure of V. hederaceae leaf cyclotide-1 ( vhl-1), a leaf-specific expressed 31-residue cyclotide, has been determined using two-dimensional H-1 NMR spectroscopy. vhl-1 adopts a compact and well defined structure including a distorted triple-stranded β- sheet, a short 310 helical segment and several turns. It is stabilized by three disulfide bonds, which, together with backbone segments, form a cyclic cystine knot motif. The three-disulfide bonds are almost completely buried into the protein core, and the six cysteines contribute only 3.8% to the molecular surface. A pH titration experiment revealed that the folding of vhl-1 shows little pH dependence and allowed the pK(a) of 3.0 for Glu(3) and &SIM; 5.0 for Glu(14) to be determined. Met(7) was found to be oxidized in the native form, consistent with the fact that its side chain protrudes into the solvent, occupying 7.5% of the molecular surface. vhl-1 shows anti-HIV activity with an EC50 value of 0.87 μ m.

Leading coordinate analysis of reaction pathways in proton chain transfer: Application to a two-proton transfer model for the green fluorescent protein

The ‘leading coordinate’ approach to computing an approximate reaction pathway, with subsequent determination of the true minimum energy profile, is applied to a two-proton chain transfer model based on the chromophore and its surrounding moieties within the green fluorescent protein (GFP). Using an ab initio quantum chemical method, a number of different relaxed energy profiles are found for several plausible guesses at leading coordinates. The results obtained for different trial leading coordinates are rationalized through the calculation of a two-dimensional relaxed potential energy surface (PES) for the system. Analysis of the 2-D relaxed PES reveals that two of the trial pathways are entirely spurious, while two others contain useful information and can be used to furnish starting points for successful saddle-point searches. Implications for selection of trial leading coordinates in this class of proton chain transfer reactions are discussed, and a simple diagnostic function is proposed for revealing whether or not a relaxed pathway based on a trial leading coordinate is likely to furnish useful information.

On the construction of correlation functions for the integrable supersymmetric fermion models

We review the recent progress on the construction of the determinant representations of the correlation functions for the integrable supersymmetric fermion models. The factorizing F-matrices (or the so-called F-basis) play an important role in the construction. In the F-basis, the creation (and the annihilation) operators and the Bethe states of the integrable models are given in completely symmetric forms. This leads to the determinant representations of the scalar products of the Bethe states for the models. Based on the scalar products, the determinant representations of the correlation functions may be obtained. As an example, in this review, we give the determinant representations of the two-point correlation function for the U-q(gl(2 vertical bar 1)) (i.e. q-deformed) supersymmetric t-J model. The determinant representations are useful for analyzing physical properties of the integrable models in the thermodynamical limit.

On the statistical analysis of the GS-NS0 cell proteome: Imputation, clustering and variability testing

We have undertaken two-dimensional gel electrophoresis proteomic profiling on a series of cell lines with different recombinant antibody production rates. Due to the nature of gel-based experiments not all protein spots are detected across all samples in an experiment, and hence datasets are invariably incomplete. New approaches are therefore required for the analysis of such graduated datasets. We approached this problem in two ways. Firstly, we applied a missing value imputation technique to calculate missing data points. Secondly, we combined a singular value decomposition based hierarchical clustering with the expression variability test to identify protein spots whose expression correlates with increased antibody production. The results have shown that while imputation of missing data was a useful method to improve the statistical analysis of such data sets, this was of limited use in differentiating between the samples investigated, and highlighted a small number of candidate proteins for further investigation. (c) 2006 Elsevier B.V. All rights reserved.

Saponins from Quillaja saponaria Molina: Isolation, Characterization and Ability to Form Immuno Stimulatory Complexes (ISCOMs)

ISCOMs have received much attention as vaccine adjuvants due to their immunostimulatory effects. They are colloidal particles typically comprised of phospholipids, cholesterol and Quil A, a crude mixture of saponins extracted from the bark of Quillaja saponaria Molina. We have previously shown that ISCOMs can be prepared by ether injection wherein an ether solution of phospholipids and cholesterol in a mass ratio of 5:2 is injected into a solution of Quil A at a mass ratio of 7 lipids: 3 Quil A. The aim of this study was firstly to isolate and characterise discrete fractions of Quil A and secondly to investigate which of these fractions were able to form ISCOMs by the method of ether injection. Six fractions of Quil A were isolated by semi-preparative reverse phase high performance liquid chromatography (RP-HPLC) and characterised by analytical HPLC, liquid chromatography tandem mass spectrometry (LC-MS) and the qualitative Liebermann- Burchard and Molisch tests for triterpenoids and carbohydrates respectively. ISCOMs were subsequently prepared from the isolated fractions by the method of ether injection and the resulting preparations characterized by photon correlation spectroscopy (PCS) and negative stain transmission electron microscopy (TEM). The molecular weights of the major compounds in the fractions ranged from ∼1200 to ∼2300 Da; all fractions tested positive for triterpenoids and saccharides and four of the fractions were identified as QS-7, QS-17, QS-18 and QS-21 by analysis (LC-MS and analytical HPLC). Injection of ether solutions of lipids into aqueous solutions of QS-17, QS-18 or QS-21 all resulted in homogeneous ISCOM dispersions. The combination of lipids and QS-7 by ether injection produced lamellae and liposomes as the prominent structures and a minor amount of ISCOMs. The remaining two hydrophilic, low molecular weight fractions of Quil A did not produce ISCOMs, instead liposomes and helical structures predominated in the samples.

Studies on Wilson loops, correlators and localization in supersymmetric quantum field theories

In this thesis we study at perturbative level correlation functions of Wilson loops (and local operators) and their relations to localization, integrability and other quantities of interest as the cusp anomalous dimension and the Bremsstrahlung function. First of all we consider a general class of 1/8 BPS Wilson loops and chiral primaries in N=4 Super Yang-Mills theory. We perform explicit two-loop computations, for some particular but still rather general configuration, that confirm the elegant results expected from localization procedure. We find notably full consistency with the multi-matrix model averages, obtained from 2D Yang-Mills theory on the sphere, when interacting diagrams do not cancel and contribute non-trivially to the final answer. We also discuss the near BPS expansion of the generalized cusp anomalous dimension with L units of R-charge. Integrability provides an exact solution, obtained by solving a general TBA equation in the appropriate limit: we propose here an alternative method based on supersymmetric localization. The basic idea is to relate the computation to the vacuum expectation value of certain 1/8 BPS Wilson loops with local operator insertions along the contour. Also these observables localize on a two-dimensional gauge theory on S^2, opening the possibility of exact calculations. As a test of our proposal, we reproduce the leading Luscher correction at weak coupling to the generalized cusp anomalous dimension. This result is also checked against a genuine Feynman diagram approach in N=4 super Yang-Mills theory. Finally we study the cusp anomalous dimension in N=6 ABJ(M) theory, identifying a scaling limit in which the ladder diagrams dominate. The resummation is encoded into a Bethe-Salpeter equation that is mapped to a Schroedinger problem, exactly solvable due to the surprising supersymmetry of the effective Hamiltonian. In the ABJ case the solution implies the diagonalization of the U(N) and U(M) building blocks, suggesting the existence of two independent cusp anomalous dimensions and an unexpected exponentation structure for the related Wilson loops.