Prediction of Golgi Type II membrane proteins based on their transmembrane domains

Motivation: A major issue in cell biology today is how distinct intracellular regions of the cell, like the Golgi Apparatus, maintain their unique composition of proteins and lipids. The cell differentially separates Golgi resident proteins from proteins that move through the organelle to other subcellular destinations. We set out to determine if we could distinguish these two types of transmembrane proteins using computational approaches. Results: A new method has been developed to predict Golgi membrane proteins based on their transmembrane domains. To establish the prediction procedure, we took the hydrophobicity values and frequencies of different residues within the transmembrane domains into consideration. A simple linear discriminant function was developed with a small number of parameters derived from a dataset of Type II transmembrane proteins of known localization. This can discriminate between proteins destined for Golgi apparatus or other locations (post-Golgi) with a success rate of 89.3% or 85.2%, respectively on our redundancy-reduced data sets.

The spectrum of minimal defining sets of some Steiner systems

For a design D, define spec(D) = {\M\ \ M is a minimal defining set of D} to be the spectrum of minimal defining sets of D. In this note we give bounds on the size of an element in spec(D) when D is a Steiner system. We also show that the spectrum of minimal defining sets of the Steiner triple system given by the points and lines of PG(3,2) equals {16,17,18,19,20,21,22}, and point out some open questions concerning the Steiner triple systems associated with PG(n, 2) in general. (C) 2002 Elsevier Science B.V. All rights reserved.

Skolem-type difference sets for cycle systems

Cyclic m-cycle systems of order v are constructed for all m greater than or equal to 3, and all v = 1(mod 2m). This result has been settled previously by several authors. In this paper, we provide a different solution, as a consequence of a more general result, which handles all cases using similar methods and which also allows us to prove necessary and sufficient conditions for the existence of a cyclic m-cycle system of K-v - F for all m greater than or equal to 3, and all v = 2(mod 2m).

Computational differentiation of N-terminal signal peptides and transmembrane helices

Signal peptides and transmembrane helices both contain a stretch of hydrophobic amino acids. This common feature makes it difficult for signal peptide and transmembrane helix predictors to correctly assign identity to stretches of hydrophobic residues near the N-terminal methionine of a protein sequence. The inability to reliably distinguish between N-terminal transmembrane helix and signal peptide is an error with serious consequences for the prediction of protein secretory status or transmembrane topology. In this study, we report a new method for differentiating protein N-terminal signal peptides and transmembrane helices. Based on the sequence features extracted from hydrophobic regions (amino acid frequency, hydrophobicity, and the start position), we set up discriminant functions and examined them on non-redundant datasets with jackknife tests. This method can incorporate other signal peptide prediction methods and achieve higher prediction accuracy. For Gram-negative bacterial proteins, 95.7% of N-terminal signal peptides and transmembrane helices can be correctly predicted (coefficient 0.90). Given a sensitivity of 90%, transmembrane helices can be identified from signal peptides with a precision of 99% (coefficient 0.92). For eukaryotic proteins, 94.2% of N-terminal signal peptides and transmembrane helices can be correctly predicted with coefficient 0.83. Given a sensitivity of 90%, transmembrane helices can be identified from signal peptides with a precision of 87% (coefficient 0.85). The method can be used to complement current transmembrane protein prediction and signal peptide prediction methods to improve their prediction accuracies. (C) 2003 Elsevier Inc. All rights reserved.

Signal trait sexual dimorphism and mutual sexual selection in Drosophila serrata

The evolution of sexual dimorphism may occur when natural and sexual selection result in different optimum trait values for males and females. Perhaps the most prominent examples of sexual dimorphism occur in sexually selected traits, for which males usually display exaggerated trait levels, while females may show reduced expression of the trait. In some species, females also exhibit secondary sexual traits that may either be a consequence of a correlated response to sexual selection on males or direct sexual selection for female secondary sexual traits. In this experiment, we simultaneously measure the intersex genetic correlations and the relative strength of sexual selection on males and females for a set of cuticular hydrocarbons in Drosophila serrata. There was significant directional sexual selection on both male and female cuticular hydrocarbons: the strength of sexual selection did not differ among the sexes but males and females preferred different cuticular hydrocarbons. In contrast with many previous studies of sexual dimorphism, intersex genetic correlations were low. The evolution of sexual dimorphism in D. serrata appears to have been achieved by sex-limited expression of traits controlled by genes on the X chromosome and is likely to be in its final stages.

An advanced method for eliminating impacts from frequency deviations in power system signal processing

Frequency deviation is a common problem for power system signal processing. Many power system measurements are carried out in a fixed sampling rate assuming the system operates in its nominal frequency (50 or 60 Hz). However, the actual frequency may deviate from the normal value from time to time due to various reasons such as disturbances and subsequent system transients. Measurement of signals based on a fixed sampling rate may introduce errors under such situations. In order to achieve high precision signal measurement appropriate algorithms need to be employed to reduce the impact from frequency deviation in the power system data acquisition process. This paper proposes an advanced algorithm to enhance Fourier transform for power system signal processing. The algorithm is able to effectively correct frequency deviation under fixed sampling rate. Accurate measurement of power system signals is essential for the secure and reliable operation of power systems. The algorithm is readily applicable to such occasions where signal processing is affected by frequency deviation. Both mathematical proof and numerical simulation are given in this paper to illustrate robustness and effectiveness of the proposed algorithm. Crown Copyright (C) 2003 Published by Elsevier Science B.V. All rights reserved.

Constitutively active signal transducer and activator of transcription 5 can replace the requirement for growth hormone in adipogenesis of 3T3-F442A preadipocytes

Although it is the best characterized in vitro model of GH action, the mechanisms used by GH to induce differentiation of murine 3T3-F442A preadipocytes remain unclear. Here we have examined the role of three transcriptional regulators in adipogenesis. These regulators are either rapidly induced in response to GH [Stra13, signal transducer and activator of transcription (Stat) 3] or of central importance to GH signaling (Stat5). Retroviral transfection of 3T3-F442A preadipocytes was used to increase expression of Stra13, Stat3, and Stat5a. Only Stat5a transfection increased the expression of adipogenic markers peroxisome proliferator-activated receptor gamma, CCAAT enhancer binding protein (C/EBP)alpha, and adipose protein 2/fatty acid-binding protein in response to GH, as determined by quantitative RT-PCR. Transfection with constitutively active Stat3 and Stat5a revealed that constitutively active Stat5a but not Stat3 was able to replace the GH requirement for adipogenesis. Constitutively active Stat5a but not Stat3 was able to increase the formation of lipid droplets and expression of alpha-glycerol phosphate dehydrogenase toward levels seen in mature adipocytes. Constitutively active Stat5a was also able to increase the expression of transcripts for C/EBPalpha to similar levels as GH, and of C/EBPbeta, peroxisome proliferator-activated receptor gamma, and adipose protein 2/fatty acid-binding protein transcripts to a lesser extent. An in vivo role for GH in murine adipogenesis is supported by significantly decreased epididymal fat depot size in young GH receptor-deleted mice, before manifestation of the lipolytic actions of GH. We conclude that Stat5 is a critical factor in GH-induced, and potentially prolactin-induced, murine adipogenesis.

Large sets of large sets of Steiner triple systems of order 9

We describe a direct method of partitioning the 840 Steiner triple systems of order 9 into 120 large sets. The method produces partitions in which all of the large sets are isomorphic and we apply the method to each of the two non-isomorphic large sets of STS(9).

Adapted Gaussian basis sets for atoms from Li through Xe generated with the generator coordinate Hartree-Fock method

Utiliza-se o método coordenada geradora Hartree-Fock para gerar bases Gaussianas adaptadas para os átomos de Li (Z=3) até Xe (Z=54). Neste método, integram-se as equações de Griffin-Hill-Wheeler-Hartree-Fock através da técnica de discretização integral. Comparam-se as funções de ondas geradas neste trabalho com as funções de ondas Roothaan-Hartree-Fock de Clementi e Roetti (1974) e com outros conjuntos de bases relatados na literatura. Para os átomos estudados aqui, os erros em nossas energias totais relativos aos limites numéricos Hartree-Fock são sempre menores que 7,426 milihartree.

Improving fECG signal acquisition in the evaluation of fetal well-being

The ability to monitor fetal heart rate is vital during late pregnancy and labor in order to evaluate fetal well-being. Current monitoring practice is essentially based on external cardiotocography and, less frequently, during labor, invasive fetal scalp electrocardiography. Many current and envisaged applications could benefi t from simpler devices using a 3-lead ECG confi guration. We are designing a maternity support belt with an embedded wireless 3-lead ECG sensor, and have investigated the infl uence of the ground electrode position on signal quality. Data from over 100 pregnant women was collected with the ground electrode placed in 3 locations in order to determine optimum electrode placement and belt form factor.

A two terminal optical signal and image processing p-i-n/p-i-n image and colour sensor

A two terminal optically addressed image processing device based on two stacked sensing/switching p-i-n a-SiC:H diodes is presented. The charge packets are injected optically into the p-i-n sensing photodiode and confined at the illuminated regions changing locally the electrical field profile across the p-i-n switching diode. A red scanner is used for charge readout. The various design parameters and addressing architecture trade-offs are discussed. The influence on the transfer functions of an a-SiC:H sensing absorber optimized for red transmittance and blue collection or of a floating anode in between is analysed. Results show that the thin a-SiC:H sensing absorber confines the readout to the switching diode and filters the light allowing full colour detection at two appropriated voltages. When the floating anode is used the spectral response broadens, allowing B&W image recognition with improved light-to-dark sensitivity. A physical model supports the image and colour recognition process.

New stacked photodevices for signal multiplexing and demultiplexing applications in the visible spectrum

Results on the use of a double a-SiC:H p-i-n heterostructure for signal multiplexing and demultiplexing applications in the visible range are presented. Pulsed monochromatic beams together (multiplexing mode), or a single polychromatic beam (demultiplexing mode) impinge on the device and are absorbed, accordingly to their wavelength. Red, green and blue pulsed input channels are transmitted together, each one with a specific transmission rate. The combined optical signal is analyzed by reading out, under different applied voltages, the generated photocurrent. Results show that in the multiplexing mode the output signal is balanced by the wavelength and transmission rate of each input channel, keeping the memory of the incoming optical carriers. In the demultiplexing mode the photocurrent is controlled by the applied voltage allowing regaining the transmitted information. A physical model supported by a numerical simulation gives insight into the device operation.