Position Of Domain Boundaries Research Articles

Topography prediction of helical transmembrane proteins by a new modification of the sliding window method.

Protein functions are specified by its three-dimensional structure, which is usually obtained by X-ray crystallography. Due to difficulty of handling membrane proteins experimentally to date the structure has only been determined for a very limited part of membrane proteins (<4%). Nevertheless, investigation of structure and functions of membrane proteins is important for medicine and pharmacology and, therefore, is of significant interest. Methods of computer modeling based on the data on the primary protein structure or the symbolic amino acid sequence have become an actual alternative to the experimental method of X-ray crystallography for investigating the structure of membrane proteins. Here we presented the results of the study of 35 transmembrane proteins, mainly GPCRs, using the novel method of cascade averaging of hydrophobicity function within the limits of a sliding window. The proposed method allowed revealing 139 transmembrane domains out of 140 (or 99.3%) identified by other methods. Also 236 transmembrane domain boundary positions out of 280 (or 84%) were predicted correctly by the proposed method with deviation from the predictions made by other methods that does not exceed the detection error of this method.

Medium-Throughput Processing of Whole Mount In Situ Hybridisation Experiments into Gene Expression Domains

Understanding the function and evolution of developmental regulatory networks requires the characterisation and quantification of spatio-temporal gene expression patterns across a range of systems and species. However, most high-throughput methods to measure the dynamics of gene expression do not preserve the detailed spatial information needed in this context. For this reason, quantification methods based on image bioinformatics have become increasingly important over the past few years. Most available approaches in this field either focus on the detailed and accurate quantification of a small set of gene expression patterns, or attempt high-throughput analysis of spatial expression through binary pattern extraction and large-scale analysis of the resulting datasets. Here we present a robust, “medium-throughput” pipeline to process in situ hybridisation patterns from embryos of different species of flies. It bridges the gap between high-resolution, and high-throughput image processing methods, enabling us to quantify graded expression patterns along the antero-posterior axis of the embryo in an efficient and straightforward manner. Our method is based on a robust enzymatic (colorimetric) in situ hybridisation protocol and rapid data acquisition through wide-field microscopy. Data processing consists of image segmentation, profile extraction, and determination of expression domain boundary positions using a spline approximation. It results in sets of measured boundaries sorted by gene and developmental time point, which are analysed in terms of expression variability or spatio-temporal dynamics. Our method yields integrated time series of spatial gene expression, which can be used to reverse-engineer developmental gene regulatory networks across species. It is easily adaptable to other processes and species, enabling the in silico reconstitution of gene regulatory networks in a wide range of developmental contexts.

Prediction of Number and Position of Domain Boundaries in Multi-Domain Proteins by Use of Amino Acid Sequence Alone

Prediction of protein domain boundaries is an important step for the prediction of three-dimensional structure. The simple method PDP has been elaborated for prediction of the number and position of domain boundaries in multi-domain proteins by use of amino acid sequence alone. The method uses an optimized scale based on the statistics of appearance of amino acid residues at domain boundaries. Our method demonstrates promising results in comparison to other methods that do not use homologous sequences. From the database of proteins that are targets from CASP6 (Critical Assessment of Techniques for Protein Structure Prediction) our program correctly assigned the number of domains for approximately 80% of one domain proteins and approximately 50% for two-domain proteins. Our method offers three main advantages: it is very simple, it is fast, and it uses a minimal number of parameters in comparison with other methods.

Dynamic control of positional information in the early Drosophila embryo.

Morphogen gradients contribute to pattern formation by determining positional information in morphogenetic fields. Interpretation of positional information is thought to rely on direct, concentration-threshold-dependent mechanisms for establishing multiple differential domains of target gene expression. In Drosophila, maternal gradients establish the initial position of boundaries for zygotic gap gene expression, which in turn convey positional information to pair-rule and segment-polarity genes, the latter forming a segmental pre-pattern by the onset of gastrulation. Here we report, on the basis of quantitative gene expression data, substantial anterior shifts in the position of gap domains after their initial establishment. Using a data-driven mathematical modelling approach, we show that these shifts are based on a regulatory mechanism that relies on asymmetric gap-gap cross-repression and does not require the diffusion of gap proteins. Our analysis implies that the threshold-dependent interpretation of maternal morphogen concentration is not sufficient to determine shifting gap domain boundary positions, and suggests that establishing and interpreting positional information are not independent processes in the Drosophila blastoderm.

Surface Characters of Interfaces and Twin Domains: TEM and AFM Study of a Feldspar Crystal

Alkali feldspar, a framework silicate (K, Na)(Si3Al)04, is a common component in ceramic materials. The feldspar crystals commonly display exsolution lamellae, twins, and modulated structures. The boundaries between neighboring domains may cause stain energy. The domain structures cause heterogeneities both inside crystals and on crystal surfaces in aspects of structure, composition, and surface microtopography. Reactivity at domain boundary positions is different from the neighboring areas. More and more studies show the effects of microtopography on the surface reactivity. It is important to reveal the surface characters or microtopography of domain structures in crystals, and their effects on local reactivity.Results from transmission electron microscopy (TEM) characterization show it contains exsolution lamellae (both K-rich and Na-rich lamellae) and twin domains in the Na-rich lamellae (Fig. 1A). Its SAED pattern shows reflections from both K-rich and Na-rich lamellae (Fig. B). Splitted reflections result from the Na-rich lamellae wiht twin domains related by (010) mirror plane, i.e., albite twin law.

A new commensurate modulated structure in orthoclase

Transmission electron microscopy shows that there is an ordered modulated structure in orthoclase (Or84.6Ab13.1An2.3) (Or = orthoclase, Ab = albite, An = anorthite) of an augite monzonite from Wulian, Shandong Province, Northern China. The modulated orthoclase is composed of a series of triclinic (010) layer domains with C\overline 1 symmetry. Each domain has a thickness of 4d010 and the domains are periodically arranged along the b axis. The modulation period along the b axis is thus 104 A (= 8d010). The relationship between the extended unit-cell parameters of the modulated structure (supercell) and the triclinic subcell parameters is: asup \simeqasub; bsup = 8d010 \simeq 8bsub; Csup \simeq Csub; βsup \simeq βsub. The probable space group of the commensurately modulated orthoclase is Pm. The modulated structure probably forms during the phase transition from sanidine (C2/m symmetry) to microcline (C\overline 1 symmetry) through the segregation of Al atoms from T2 sites into T1(0) and T1(m) sites, respectively, in neighboring domains, which are in the albite-twin relationship. The ordering of Al atoms in the tetrahedral sites during the phase transition results in a sinusoidal deviation of the crystal structure from monoclinic symmetry. The Al–Si distribution near the domain boundary positions is likely to be relatively disordered.

The nature of the planar instability and pattern selection mechanisms attending directional thin film alloy solidification

This reports on a study of the planar instability and the dynamics of the subsequent cellular pattern evolution on oriented and non-oriented alloy single crystals of succinonitrile-salol (S-Sa), succinonitrile-acetone (S-A) and pivalic acid-ethanol (P-E) alloys in directional solidification. Stable and unstable patterns for a total of 200 combinations of composition X 0, gradient G and velocity v have been recorded. The detailed systematics is reported elsewhere. In the near marginal range the wavelength and amplitude increase with v, both entering a decreasing mode at higher v. Upon jump-starting, it has been found that the planar breakdown invariably emanates from the ever-present adjacent grain or domain boundary positions. The microscopic imperfection at a boundary position spontaneously grooves as the velocity is jumped from zero and ultimately induces a non-uniform finite amplitude perturbation with sidebands of Mullins and Sekerka scale across an adjacent interface which contains a rich mix of wavenumbers. As the amplitude reaches the order of the wavelength, Ostwald ripening usually ensues wherein roughly every second wave is overgrown. For high supersaturations this wavelength doubling is repeated. The growth velocity for onset of a planar instability observed experimentally is close to that predicted by the constitutional supercooling criterion and by the thin film version of Mullins and Sekerka linear stability analysis. Within the long-lived transient state, tip-splitting, overgrowth and solitons generated spontaneously in oriented crystals ultimately adjust the cellular wavelength, amplitude and tip radius to relatively uniform, stable endpoint values. Kink manifestations or solitons which are almost stationary in the crystal frame of reference play a critical role in the final stages of a selected pattern whose wavelength is always larger than that of the initiating perturbation.

Statistical Study of the Barkhausen Effect Part II, Relation between Domain Size and Internal Stress

The numerical values for domain size, obtained in Part I, were discussed, in comparison with the results by Bloch's theory of ellipsoidal domain. It was concluded that the distribution of internal stress plays a leading role in the determination of the remaining position of domain boundary. The distribution of internal stress were determined from the standpoint of the probability theory. Domain size distribution formulae, showing the experimental regularties between the impulse size and the search-coil length, as described in Part I, were deduced from consideration on the relations between the distribution of internal stress and that of domain boundary.