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PubMed2005

Target selection of soluble protein complexes for structural proteomics studies.

BACKGROUND: Protein expression in E. coli is the most commonly used system to produce protein for structural studies, because it is fast and inexpensive and can produce large quantity of proteins. However, when proteins from other species such as mammalian are produced in this system, problems of protein expression and solubility arise 1. Structural genomics project are currently investigating proteomics pipelines that would produce sufficient quantities of recombinant proteins for structural studies of protein complexes. To investigate how the E. coli protein expression system could be used for this purpose, we purified apoptotic binary protein complexes formed between members of the Caspase Associated Recruitment Domain (CARD) family. RESULTS: A combinatorial approach to the generation of protein complexes was performed between members of the CARD domain protein family that have the ability to form hetero-dimers between each other. In our method, each gene coding for a specific protein partner is cloned in pET-28b (Novagen) and PGEX2T (Amersham) expression vectors. All combinations of protein complexes are then obtained by reconstituting complexes from purified components in native conditions, after denaturation-renaturation or co-expression. Our study applied to 14 soluble CARD domain proteins revealed that co-expression studies perform better than native and denaturation-renaturation methods. In this study, we confirm existing interactions obtained in vivoin mammalian cells and also predict new interactions. CONCLUSION: The simplicity of this screening method could be easily scaled up to identify soluble protein complexes for structural genomic projects. This study reports informative statistics on the solubility of human protein complexes expressed in E.coli belonging to the human CARD protein family.

Journal Article↗

PubMed1998

Retinoid X receptor and c-cerbA/thyroid hormone receptor regulate erythroid cell growth and differentiation.

Nuclear receptors are important regulators of erythroid cell development. Here we investigated the impact of retinoid X receptor (RXR), retinoic acid receptor (RAR), and of the c-erbA/thyroid hormone (T3) receptor (c-erbA/TR) on growth and differentiation of erythroid cells using an in vitro culture system of stem cell factor-dependent erythroid progenitors. RXR, RAR, and c-erbA/TR-specific ligands were found to induce erythroid-specific gene expression and to accelerate erythroid differentiation in culture, with T3 being most effective. Furthermore, while ligand-activated c-erbA/TR accelerated differentiation, unliganded c-erbA/TR effectively blocked differentiation and supported sustained progenitor growth in culture. Thus, c-erbA/TR appears to act as a binary switch affecting erythroid cell fate: unliganded c-erbA/TR supports growth while ligand-activated c-erbA/TR induces differentiation. Additionally, to determine the impact of RXR for erythroid cell development, dominant interfering mutant RXRs, lacking the transcriptional activator functions AF-1 and AF-2, or AF-2 only, or the entire DNA-binding domain, were introduced into erythroid progenitor cells via recombinant retrovirus vectors and analyzed for RXR-specific effects. It was found that expression of wild-type RXR and of the RXR mutants devoid of AF-1 and/or AF-2 supported a transient outgrowth of erythroid cells. In marked contrast, expression of the dominant interfering deltaDNA-binding domain RXR, containing a deletion of the entire DNA-binding domain, was incompatible with erythroid cell growth in vitro, suggesting a pivotal role of RXR for erythroid cell development.

Animals↗

PubMed1999

Layer-by-layer deposition of oppositely charged polyelectrolytes on the surface of condensed DNA particles.

DNA can be condensed with an excess of poly-cations in aqueous solutions forming stable particles of submicron size with positive surface charge. This charge surplus can be used to deposit alternating layers of polyanions and polycations on the surface surrounding the core of condensed DNA. Using poly-L-lysine (PLL) and succinylated PLL (SPLL) as polycation and polyanion, respectively, we demonstrated layer-by-layer architecture of the particles. Polyanions with a shorter carboxyl/backbone distance tend to disassemble binary DNA/PLL complexes by displacing DNA while polyanions with a longer carboxyl/backbone distance effectively formed a tertiary complex. The zeta potential of such complexes became negative, indicating effective surface recharging. The charge stoichiometry of the DNA/PLL/SPLL complex was found to be close to 1:1:1, resembling poly-electrolyte complexes layered on macrosurfaces. Recharged particles containing condensed plasmid DNA may find applications as non-viral gene delivery vectors.

Anions↗

PubMed2002

Parallel image restoration with a two-dimensional likelihood-based algorithm.

We describe a pixelwise parallel algorithm for the restoration of images that have been corrupted by a low-pass optical channel and additive noise. This new algorithm is based on an iterative soft-decision method of error correction (i.e., turbo decoding) and offers performance on binary-valued imagery that is comparable to the Viterbi algorithm. We quantify the restoration performance of this new algorithm on random binary imagery for which it is superior to both the Wiener filter and the projection onto convex sets algorithms over a wide range of channels. For typical optical channels, the new algorithm is within 0.5 dB of the two-dimensional Viterbi restoration method [J. Opt. Soc. Am. A 17, 265 (2000)]. We also demonstrate the extension of our new algorithm to correlated and gray-scale images using vector quantization to mitigate the associated complexity burden. A highly parallel focal-plane implementation is also discussed, and a design study is presented to quantify the capabilities of such a VLSI hardware solution. We find that video-rate restoration on 252 x 252 pixel images is possible using current technology.

Journal Article↗

PubMed2004

Improved protein secondary structure prediction using support vector machine with a new encoding scheme and an advanced tertiary classifier.

Prediction of protein secondary structures is an important problem in bioinformatics and has many applications. The recent trend of secondary structure prediction studies is mostly based on the neural network or the support vector machine (SVM). The SVM method is a comparatively new learning system which has mostly been used in pattern recognition problems. In this study, SVM is used as a machine learning tool for the prediction of secondary structure and several encoding schemes, including orthogonal matrix, hydrophobicity matrix, BLOSUM62 substitution matrix, and combined matrix of these, are applied and optimized to improve the prediction accuracy. Also, the optimal window length for six SVM binary classifiers is established by testing different window sizes and our new encoding scheme is tested based on this optimal window size via sevenfold cross validation tests. The results show 2% increase in the accuracy of the binary classifiers when compared with the instances in which the classical orthogonal matrix is used. Finally, to combine the results of the six SVM binary classifiers, a new tertiary classifier which combines the results of one-versus-one binary classifiers is introduced and the performance is compared with those of existing tertiary classifiers. According to the results, the Q3 prediction accuracy of new tertiary classifier reaches 78.8% and this is better than the best result reported in the literature.

Algorithms↗

PubMed2005

Hyper-Rayleigh spectral intensities of gaseous Kr-Xe mixture.

Binary collision-induced hyper-Rayleigh (CIHR) spectra of Kr-Xe gaseous system are computed quantum mechanically and classically within the frequency range up to 380 cm(-1). The intensities are expressed in absolute units. The details of the theory developed for the CIHR spectra are given and the properties of the profiles as well as the depolarization ratio frequency dependence are discussed. The contributions to the spectra related to the vector b10(r) and the septor b30(r) components of the hyperpolarizability tensor are evaluated.

Journal Article↗

PubMed2001

A normed space of genetic operators with applications to scalability issues.

We define an abstract normed vector space where the genetic operators are elements. This is used to define the disturbance of the generational operator G as the distance between the crossover and mutation operator (combined) and the identity. This quantity appears in a bound on the variance of fixed-point populations, and in a bound on the force //v - G(v)// that applies to the optimal population v. When analyzed for the case of fixed-length binary strings, a connection is shown between these measures and the size of the search space. Guides for parameter settings are given, if population convergence is required as the string length tends to infinity.

Cross-Over Studies↗

PubMedDate not supplied

Hybrid formation between African trypanosomes during cyclical transmission.

Trypanosomes of the species Trypanosoma brucei reproduce primarily by binary fission, but the frequency of enzyme electrophoretic variants in natural populations of T. brucei has provided indirect evidence for the existence of a sexual cycle. These studies, coupled with studies of restriction fragment length polymorphisms of genes encoding glycolytic enzymes, have also provided evidence for T. brucei being diploid. Here we report direct evidence of gene exchange between two different clones of trypanosomes after mixed infection and full cyclical development in the tsetse fly vector.

Animals↗

PubMed2000

Diffuse X-ray scattering and disorder in p-methyl-N-(p-chlorobenzylidene)aniline, C14H12ClN (ClMe): analysis via automatic refinement of a Monte Carlo model

A recently developed method for fitting a Monte Carlo computer simulation model to observed single-crystal diffuse X-ray scattering has been applied to (h0l) scattering data obtained for the disordered compound p-methyl-N-(p-chlorobenzylidene)aniline, C14H12ClN (ClMe), at 295 K. Each molecular site is occupied by a molecule in one of four basically different orientations defined by combinations of a side-to-side and an end-to-end flip. These different orientations were represented in the model by two sets of binary random variables. In addition to these occupancy variables, the model also allowed local orientational and centre-of-mass translational displacements. The disordered structure was modelled using rigid-body molecules linked by harmonic springs to represent 'effective' intermolecular interactions. The refined model included 4 parameters describing the correlation of neighbouring occupational variables and 28 parameters describing the force-constant and 'size-effect' parameters on seven symmetry-inequivalent types of intermolecular vectors. The model refined to an overall agreement factor, [formula: see text], of 32.8% for 28,500 data points. It was found that the SRO correlation structure observed within the layers of molecules in the ab plane is typical of a frustrated lattice, where nearest- and second-nearest-neighbour effects oppose each other. This appears to be the main difference between this compound and the sister compound, p-chloro-N-(p-methylbenzylidene)aniline (MeCl), studied previously. The local relaxational displacements that result from local 'size-effect' strains operating on different intermolecular vectors generally reflect the tendency for distances involving Cl-Cl interactions to be longer than the observed average distances.

Journal Article↗

PubMed2006

Gene expression from random libraries of yeast promoters.

Genomewide techniques to assay gene expression and transcription factor binding are in widespread use, but are far from providing predictive rules for the function of regulatory DNA. To investigate more intensively the grammar rules for active regulatory sequence, we made libraries from random ligations of a very restricted set of sequences. Working with the yeast Saccharomyces cerevisiae, we developed a novel screen based on the sensitivity of ascospores lacking dityrosine to treatment with lytic enzymes. We tested two separate libraries built by random ligation of a single type of activator site either for a well-characterized sporulation factor, Ndt80, or for a new sporulation-specific regulatory site that we identified and several neutral spacer elements. This selective system achieved up to 1:10(4) enrichment of the artificial sequences that were active during sporulation, allowing a high-throughput analysis of large libraries of synthetic promoters. This is not practical with methods involving direct screening for expression, such as those based on fluorescent reporters. There were very few false positives, since active promoters always passed the screen when retested. The survival rate of our libraries containing roughly equal numbers of spacers and activators was a few percent that of libraries made from activators alone. The sequences of approximately 100 examples of active and inactive promoters could not be distinguished by simple binary rules; instead, the best model for the data was a linear regression fit of a quantitative measure of gene activity to multiple features of the regulatory sequence.

Ether↗

PubMed2006

Clustering threshold gradient descent regularization: with applications to microarray studies.

MOTIVATION: An important goal of microarray studies is to discover genes that are associated with clinical outcomes, such as disease status and patient survival. While a typical experiment surveys gene expressions on a global scale, there may be only a small number of genes that have significant influence on a clinical outcome. Moreover, expression data have cluster structures and the genes within a cluster have correlated expressions and coordinated functions, but the effects of individual genes in the same cluster may be different. Accordingly, we seek to build statistical models with the following properties. First, the model is sparse in the sense that only a subset of the parameter vector is non-zero. Second, the cluster structures of gene expressions are properly accounted for. RESULTS: For gene expression data without pathway information, we divide genes into clusters using commonly used methods, such as K-means or hierarchical approaches. The optimal number of clusters is determined using the Gap statistic. We propose a clustering threshold gradient descent regularization (CTGDR) method, for simultaneous cluster selection and within cluster gene selection. We apply this method to binary classification and censored survival analysis. Compared to the standard TGDR and other regularization methods, the CTGDR takes into account the cluster structure and carries out feature selection at both the cluster level and within-cluster gene level. We demonstrate the CTGDR on two studies of cancer classification and two studies correlating survival of lymphoma patients with microarray expressions. AVAILABILITY: R code is available upon request. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Algorithms↗

PubMed2005

Kinetics of phase separation in thin films: simulations for the diffusive case.

We study the diffusion-driven kinetics of phase separation of a symmetric binary mixture (AB), confined in a thin-film geometry between two parallel walls. We consider cases where (i) both walls preferentially attract the same component (A), and (ii) one wall attracts and the other wall attracts (with the same strength). We focus on the interplay of phase separation and wetting at the walls, which is referred to as surface-directed spinodal decomposition (SDSD). The formation of SDSD waves at the two surfaces, with wave vectors oriented perpendicular to them, often results in a metastable layered state (also referred to as "stratified morphology"). This state is reminiscent of the situation where the thin film is still in the one-phase region but the surfaces are completely wet, and hence coated with thick wetting layers. This metastable state decays by spinodal fluctuations and crosses over to an asymptotic growth regime characterized by the lateral coarsening of pancakelike domains. These pancakes may or may not be coated by precursors of wetting layers. We use Langevin simulations to study this crossover and the growth kinetics in the asymptotic coarsening regime.

Journal Article↗

PubMed2003

Gene prediction by spectral rotation measure: a new method for identifying protein-coding regions.

A new measure for gene prediction in eukaryotes is presented. The measure is based on the Discrete Fourier Transform (DFT) phase at a frequency of 1/3, computed for the four binary sequences for A, T, C, and G. Analysis of all the experimental genes of S. cerevisiae revealed distribution of the phase in a bell-like curve around a central value, in all four nucleotides, whereas the distribution of the phase in the noncoding regions was found to be close to uniform. Similar findings were obtained for other organisms. Several measures based on the phase property are proposed. The measures are computed by clockwise rotation of the vectors, obtained by DFT for each analysis frame, by an angle equal to the corresponding central value. In protein coding regions, this rotation is assumed to closely align all vectors in the complex plane, thereby amplifying the magnitude of the vector sum. In noncoding regions, this operation does not significantly change this magnitude. Computing the measures with one chromosome and applying them on sequences of others reveals improved performance compared with other algorithms that use the 1/3 frequency feature, especially in short exons. The phase property is also used to find the reading frame of the sequence.

Chromosomes, Fungal↗

PubMed2004

alpha-Relaxation processes in binary hard-sphere mixtures.

Molecular-dynamics simulations are presented for two correlation functions formed with the partial density fluctuations of binary hard-sphere mixtures in order to explore the effects of mixing on the evolution of glassy dynamics upon compressing the liquid into high-density states. Partial-density-fluctuation correlation functions for the two species are reported. Results for the alpha-relaxation process are quantified by parameters for the strength, stretching, and time scale, where the latter varies over almost four orders of magnitude upon compression. The parameters exhibit an appreciable dependence on the wave vector, and this dependence is different for the correlation function referring to the smaller and that for the larger species. These features are shown to be in semiquantitative agreement with those calculated within the mode-coupling theory for ideal liquid-glass transitions.

Journal Article↗

PubMed1990

Dissecting the domain structure of the regulatory subunit of cAMP-dependent protein kinase I and elucidating the role of MgATP.

A truncated regulatory subunit of cAMP-dependent protein kinase I was constructed which contained deletions at both the carboxyl terminus and at the amino terminus. The entire carboxyl-terminal cAMP-binding domain was deleted as well as the first 92 residues up to the hinge region. This monomeric truncated protein still forms a complex with the catalytic subunit, and activation of this complex is mediated by cAMP. The affinity of this mutant holoenzyme for cAMP and its activation by cAMP are nearly identical to holoenzyme formed with a regulatory subunit having only the carboxyl-terminal deletion and very similar to native holoenzyme. The off rate for cAMP from both mutant regulatory subunits, however, is monophasic and very fast relative to the biphasic off rate seen for the native regulatory subunit. The effects of NaCl, urea, and pH on cAMP binding are also very similar for the mutant and native holoenzymes. Like the native type I holoenzyme, both mutant holoenzymes bind ATP with a high affinity. The positive cooperativity seen for MgATP binding to the native holoenzyme, however, is abolished in the double deletion mutant. The Hill coefficient for ATP binding to this mutant holoenzyme is 1.0 in contrast to 1.6 for the native holoenzyme. The Kd (cAMP) is increased by approximately 1 order of magnitude for both mutant forms of the holoenzyme in the presence of MgATP. A similar shift is seen for the native holoenzyme. Further characterization of the MgATP-binding properties of the wild-type holoenzyme indicates that a binary complex containing catalytic subunit and MgATP is required, in particular, for reassociation with the cAMP-bound regulatory subunit. This binary complex is required for rapid dissociation of the bound cAMP and is probably responsible for the observed reduction in cAMP-binding affinity for the type I holoenzyme in the presence of MgATP.

Adenosine Triphosphate↗

PubMed1987

Demonstration of colonies of Cowdria ruminantium in midgut epithelial cells of Amblyomma variegatum.

The development of colonies of Cowdria ruminantium was studied in midgut epithelial cells of adult Amblyomma variegatum that had become infected by feeding as nymphs on cattle with experimentally induced heart-water disease. Colonies were not observed in gut tissues obtained from nymphs during the feeding period, but were present in midgut epithelial cells of ticks obtained at 15 days after they were replete through molting to the adult stage. Colonies were small (1 to 10 micron) initially, but as tick development progressed, their diameter increased to as much as 60 micron. With electron microscopy, colonies were observed to be membrane bound and contained pleomorphic organisms that were reticulated. The organisms seemed to be dividing by binary fission. Many colonies contained a large, electron-dense inclusion that was morphologically similar to hemoglobin deposits found in the cytoplasm of midgut epithelial cells of recently fed ticks. Cowdria ruminantium was often observed adhered to these inclusions.

Animals↗

PubMed2001

A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach.

We have introduced a new method of protein secondary structure prediction which is based on the theory of support vector machine (SVM). SVM represents a new approach to supervised pattern classification which has been successfully applied to a wide range of pattern recognition problems, including object recognition, speaker identification, gene function prediction with microarray expression profile, etc. In these cases, the performance of SVM either matches or is significantly better than that of traditional machine learning approaches, including neural networks.The first use of the SVM approach to predict protein secondary structure is described here. Unlike the previous studies, we first constructed several binary classifiers, then assembled a tertiary classifier for three secondary structure states (helix, sheet and coil) based on these binary classifiers. The SVM method achieved a good performance of segment overlap accuracy SOV=76.2 % through sevenfold cross validation on a database of 513 non-homologous protein chains with multiple sequence alignments, which out-performs existing methods. Meanwhile three-state overall per-residue accuracy Q(3) achieved 73.5 %, which is at least comparable to existing single prediction methods. Furthermore a useful "reliability index" for the predictions was developed. In addition, SVM has many attractive features, including effective avoidance of overfitting, the ability to handle large feature spaces, information condensing of the given data set, etc. The SVM method is conveniently applied to many other pattern classification tasks in biology.

Computer Simulation↗

PubMed2002

The retinoblastoma gene product interacts with maintenance human DNA (cytosine-5) methyltransferase and modulates its activity.

The mammalian DNA (cytosine-5) methyltransferase (Dnmt1) is involved in the maintenance of methylation patterns in the genome during DNA replication and development. The retinoblastoma gene product, Rb, is a cell cycle regulator protein that represses transcription by recruiting histone deacetylase (HDAC1). In vivo, histone deacetylase associates with Dnmt1. Here we show that Rb itself associates with human Dnmt1 (hDnmt1) independently of its own phosphorylation status. Methyltransferase activity was co-purified with Rb. The regulatory domain of hDnmt1 binds strongly to the B and C pockets of Rb (amino acids 701-872) and inhibits methyltransferase activity by disruption of the hDnmt1-DNA binary complex. Weak interaction of Rb pockets A and B with Dnmt1 was also observed. Overexpression of Rb leads to hypomethylation of the cellular DNA, suggesting that Rb may modulate Dnmt1 activity during DNA replication in the cell cycle.

Adenoviridae↗