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The functional annotation of genomic data has become a major task for the ever-growing number of sequencing projects. In order to address this challenge, we recently developed GOblet, a free web service for the annotation of anonymous sequences with Gene Ontology (GO) terms. However, to overcome limitations of the GO terminology, and to aid in understanding not only single components but as well systemic interactions between the individual components, we have now extended the GOblet web service to integrate also pathway annotations. Furthermore, we extended and upgraded the data analysis pipeline with improved summaries, and added term enrichment and clustering algorithms. Finally, we are now making GOblet available as a stand-alone application for high-throughput processing on local machines. The advantages of this frequently requested feature is that a) the user can avoid restrictions of our web service for uploading and processing large amounts of data, and that b) confidential data can be analysed without insecure transfer to a public web server. The stand-alone version of the web service has been implemented using platform independent Tcl-scripts, which can be run with just a single runtime file utilizing the Starkit technology. The GOblet web service and the stand-alone application are freely available at http://goblet.molgen.mpg.de.

Author(s): Donna M. Muzny [1]; Steven E. Scherer (corresponding author) [1]; Rajinder Kaul [2]; Jing Wang [3]; Jun Yu [3]; Ralf Sudbrak [4, 5]; Christian J. Buhay [1]; Rui Chen [...]

Author(s): Mark T. Ross (corresponding author) [1]; Darren V. Grafham [1]; Alison J. Coffey [1]; Steven Scherer [2]; Kirsten McLay [1]; Donna Muzny [2]; Matthias Platzer [3]; Gareth R. Howell [...]

Abstract Background Several approaches can be used to determine the order of loci on chromosomes and hence develop maps of the genome. However, all mapping approaches are prone to errors either arising from technical deficiencies or lack of statistical support to distinguish between alternative orders of loci. The accuracy of the genome maps could be improved, in principle, if information from different sources was combined to produce integrated maps. The publicly available bovine genomic sequence assembly with 6× coverage (Btau_2.0) is based on whole genome shotgun sequence data and limited mapping data however, it is recognised that this assembly is a draft that contains errors. Correcting the sequence assembly requires extensive additional mapping information to improve the reliability of the ordering of sequence scaffolds on chromosomes. The radiation hybrid (RH) map described here has been contributed to the international sequencing project to aid this process. Results An RH map for the 30 bovine chromosomes is presented. The map was built using the Roslin 3000-rad RH panel (BovGen RH map) and contains 3966 markers including 2473 new loci in addition to 262 amplified fragment-length polymorphisms (AFLP) and 1231 markers previously published with the first generation RH map. Sequences of the mapped loci were aligned with published bovine genome maps to identify inconsistencies. In addition to differences in the order of loci, several cases were observed where the chromosomal assignment of loci differed between maps. All the chromosome maps were aligned with the current 6× bovine assembly (Btau_2.0) and 2898 loci were unambiguously located in the bovine sequence. The order of loci on the RH map for BTA 5, 7, 16, 22, 25 and 29 differed substantially from the assembled bovine sequence. From the 2898 loci unambiguously identified in the bovine sequence assembly, 131 mapped to different chromosomes in the BovGen RH map. Conclusion Alignment of the BovGen RH map with other published RH and genetic maps showed higher consistency in marker order and chromosome assignment than with the current 6× sequence assembly. This suggests that the bovine sequence assembly could be significantly improved by incorporating additional independent mapping information.

We investigate the photodissociation of highly excited vibrational states of water in the first absorption band. The calculation includes an ab initio potential energy surface for the A-state and an ab initio X→A transition dipole function. The bending angle is fixed at the equilibrium value within the ground electronic state. Most interesting is the high sensitivity of the final vibrational distribution of OH on the initially prepared vibrational state of H2 O. At wavelengths near the onset of the absorption spectrum the vibrational state distribution can be qualitatively understood as a Franck–Condon mapping of the initial H2 O wave function. At smaller wavelengths final state interaction in the excited state becomes stronger and the distributions become successively broader. Our calculations are in satisfactory accord with recent measurements of Vander Wal and Crim. [ABSTRACT FROM AUTHOR]

We investigated the photodissociation of methyl nitrite (CH3 ONO) and methyl thionitrite (CH3 SNO) within the first absorption band (S1 ←S0 ). The calculations were based on a two-dimensional model including the O–NO/S–NO and N=O bond distances as active coordinates. The S1 -potential energy surfaces were calculated with quantum chemical methods and the dynamical calculations were performed exactly within the time-independent approach. The main emphasis is on the origin of diffuse vibrational structure in the photoabsorption spectrum of both molecules. A low potential barrier of 0.086 eV along the O–NO dissociation coordinate in CH3 ONO prevents immediate dissociation and leads to an initial state dependent lifetime for the excited complex of 100–250 fs corresponding to 3–8 NO vibrational periods. CH3 ONO decays nonadiabatically via vibrational predissociation. The absorption spectrum of CH3 ONO is dominated by narrow Feshbach-like scattering resonances which can be characterized by two quantum numbers, m and n*: m=0 and 1 specifies the quanta of excitation in the O–NO bond and n*=0,1,2,... specifies the excited vibrational level of the N=O bond. The potential barrier is absent in CH3 SNO and the dissociation is direct on the time scale of about 10 fs corresponding to only one third of a NO vibrational period. Nevertheless, the absorption spectrum exhibits diffuse vibrational structures. The shape of the individual absorption peaks is determined by the classical Franck–Condon reflection principle. The dissociation of CH3 SNO is primarily adiabatic which leads to a pronounced energy dependence of the final NO vibrational state distribution. The diffuse structures originate in both cases from excitation of the NO stretching vibration. In order to make contact with time-dependent theory we calculated the autocorrelation function of the time-dependent wave function by inverse Fourier transformation of the... [ABSTRACT FROM AUTHOR]

We report the results of a two-dimensional, quantal study of the photodissociation of CH3O–NO within the first continuum (S0→S1, 300–400 nm) taking into account only the O–N and the N=O separations. The S1 potential energy surface is taken from recent ab initio calculations. The calculated absorption spectrum consists of two band progressions of narrow resonance lines with widths of ∼0.3 and ∼5 meV, respectively. These resonances can be associated with excitation of the O–N bond (m=0,1) and excitation of the N=O chromophore (n*=0,1,2,...). The intensities of the m=1 band are negligibly small compared to those of the m=0 band. The decay mechanism in the two cases is different: The m=0 resonances decay primarily via vibrational predissociation, i.e., a nonadiabatic transition from n* to n*-1, and yield NO products with a preferential population of the (n*-1) level. The m=1 resonances decay mainly via tunneling through a potential barrier yielding preferentially NO products in state n*. Several of the theoretical results agree qualitatively (ratio of peak intensities) or even quantitatively (energy spacing between peaks) with the measurements. Most important, however, is the good agreement found for the vibrational NO distributions at several excitation wavelengths of the parent, which reveals that vibrational predissociation within the S1 state is the main decay mechanism. [ABSTRACT FROM AUTHOR]

Vibrational state distributions following the direct photodissociation of a collinear, triatomic molecule is investigated with particular emphasis on the so-called final state interaction, i.e., the translational–vibrational coupling due to the excited state interaction potential. In order to separate the various effects which determine the state distribution we performed calculations on three levels of accuracy: The energy sudden (ES) approximation, the modified sudden (MS) approximation, and the exact close-coupling (CC) formulation. The pure ES distributions peak at high states and are very broad. They are explained within the semiclassical limit as a mapping of an amplitude onto the quantum number axis. We call this effect vibrational reflection principle in analogy to the equivalent effect in rotational excitation processes. It is a direct and sensitive probe of the parameters of the system, most importantly the potential energy surface. Energy conservation strongly modifies the ES distributions. The MS and CC distributions are much narrower and peak at considerably lower states. A detailed analysis is given within the MS approximation. Based on these general conclusions we suggest a particular excited state potential for the dissociation of CF3I which qualitatively reproduces the recently reported experimental CF3 distribution. The essential feature of this potential is a distance dependent local frequency which we find necessary to obtain distributions as broad as in the experiment. Because of the inherent difficulties with the time-of-flight technique if several energy transfer channels are involved we certainly do not know how realistic our final potential energy surface is. However, the general trends found in this study should be valid for a larger class of systems. [ABSTRACT FROM AUTHOR]

We use time-dependent quantum theory to interpret the absorption spectrum of CH3ONO in terms of the nuclear motion on the upper potential surface. The model uses one excited potential energy surface and two nuclear coordinates: the NO stretch and the CH3O–NO bond. The latter bond breaks upon excitation leading to dissociation. The spectrum consists of a broad band and two progressions corresponding to predissociation resonances. The band width is inverse proportional to the time scale on which the NO bond length increases to adjust to the longer equilibrium bond length of the upper potential energy surface. The progression of intense narrow resonances corresponds to the NO stretching motion. The other progression is due to oscillations along the reaction coordinate of the wave function temporarily trapped in the predissociation well. Our calculations show that important dynamic information can be obtained by ‘‘smearing off’’ the high resolution spectrum to generate a series of low resolution versions which reveal the time scales on which various spectral features develop in the spectrum. We also show that time-dependent theory can be used efficiently to calculate the lifetime of relatively long lived resonances. [ABSTRACT FROM AUTHOR]

Objective: To investigate the global changes accompanying human dilated cardiomyopathy (DCM) we performed a large-scale expression screen using myocardial biopsies from a group of DCM patients with moderate heart failure. By hierarchical clustering and functional annotation of the deregulated genes we examined extensive changes in the cellular and molecular processes associated to DCM. Methods: The expression profiles were obtained using a whole genome covering library (UniGene RZPD1) comprising 30 336 cDNA clones and amplified RNA from myocardiac biopsies from 10 DCM patients in comparison to tissue samples from four non-failing, healthy donors. Results: By setting stringent selection criteria 364 differentially expressed, sequence-verified non-redundant transcripts were identified with a false discovery rate of <0.001. Numerous genes and ESTs were identified representing previously recognised, as well as novel DCM-associated transcripts. Many of them were found to be upregulated and involved in cardiomyocyte energetics, muscle contraction or signalling. Two hundred and twenty-two deregulated transcripts were functionally annotated and hierarchically clustered providing an insight into the pathophysiology of DCM. Data was validated using the MLP-deficient mouse, in which several differentially expressed transcripts identified in the human DCM biopsies could be confirmed. Conclusions: We report the first genome-wide expression profile analysis using cardiac biopsies from DCM patients at various stages of the disease. Although there is a diversity of links between the cytoskeleton and the initiation of DCM, we speculate that genes implicated in intracellular signalling and in muscle contraction are associated with early stages of the disease. Altogether this study represents the most comprehensive and inclusive molecular portrait of human cardiomyopathy to date. [Copyright &y& Elsevier]