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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 [...]

Resonance Raman spectroscopy was used to examine the axial ligation of nickel(II) 5,10,15,20-tetraphenylporphyrin with pyrrolidine or piperidine. The axial ligands and their orientations influenced the type and magnitude of the calculated nonplanar distortion. Narrow and symmetric Raman lines were observed because of the similarity in macrocyclic structural parameters of the conformers and the free rotation of the axial ligands. Analysis revealed the relationship between the orientations of axial ligands and the macrocyclic distortions.

A study was conducted to examine the effects of the symmetry of substitution pattern and substituent orientations on the out-plane and in-plane distortions of the macrocyle of nickel porphyrins. These nickel porphyrins were analyzed through the use of molecular mechanics calculations, X-ray crystallography, UV visible absorption spectroscopy and resonance Raman spectroscopy. Results revealed that out-plane and in-plane distortions were dependent on perturbation symmetry of the peripheral substituents.

Research was conducted to study the influence of central metals of various sizes on the macrocyclic structure of a series of 5,15-disubstituted metallophorphyrins. Methodologies used included X-ray crystallography, resonance Raman spectroscopy and molecular mechanics. The contributions of the ruf and dom deformations in the crystal structures of several metal complexes of the phorphyrins were found to be metal-dependent. Results indicate the quantitative validity of normal-coordinate structural decomposition.

A study was conducted to examine the effects of proteins on the nonplanarity of the macrocycle in nickel cytochrome c using molecular mechanics computations and resonance Raman spectroscopy. A dual-channel spectrometer was utilized to determine RR spectra while the POLYGRAF software was used to perform molecular mechanics computations. Results indicated that the nonplanar distortion of the porphyrin of cytochromes c is supported by a small protein segment.

The effect of substituents with increasing steric demands on the structure of nickel(II) 5,15-disubstituted porphyrins was studied by X-ray crystallography, UV-visible absorption spectroscopy, resonance Raman spectroscopy, molecular energy optimization computations and INDO/s molecular orbital computations. Findings showed that the distortion of the macrocyle for the disubstituted nickel porphyrins is a combination of ruffling and doming distortions. Also, the gal distortion can be precisely described in terms of displacements along the lowest-frequency normal coordinates of B1u and A2u symmetry.

Abstract Background We present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque. Results The assembly process consisted of multiple phases: First, BACs were assembled with BAC generated sequence, then subsequently in combination with the individual overlapping WGS reads. Different assembly parameters were tested to separately optimize the performance for each BAC assembly of the BAC and WGS reads. In parallel, a second assembly was produced using only the WGS sequences and a global whole genome assembly method. The two assemblies were combined to create a more complete genome representation that retained the high quality BAC-based local assembly information, but with gaps between BACs filled in with the WGS-only assembly. Finally, the entire assembly was placed on chromosomes using the available map information. Over 90% of the assembly is now placed on chromosomes. The estimated genome size is 2.87 Gb which represents a high degree of completeness, with 95% of the available EST sequences found in assembled contigs. The quality of the assembly was evaluated by comparison to 73 finished BACs, where the draft assembly covers between 92.5 and 100% (average 98.5%) of the finished BACs. The assembly contigs and scaffolds align linearly to the finished BACs, suggesting that misassemblies are rare. Genotyping and genetic mapping of 17,482 SNPs revealed that more than 99.2% were correctly positioned within the Btau_4.0 assembly, confirming the accuracy of the assembly. Conclusion The biological analysis of this bovine genome assembly is being published, and the sequence data is available to support future bovine research.

The dansyl-C6-choline binding to the nicotinic acetylcholine receptor differs at the alphagamma and alphadelta binding sites as measured by fluorescence changes. The dissociation rates from the two sites also differ by 5-10 fold. Fluorescence is higher for the alphadelta site, which also display slower dissociation and higher affinity than the alphagamma site.

We have measured the polarized Raman cross sections and depolarization ratios of 16 fundamental modes of nickel octaethyltetraphenylporphyrin in a CS2 solution for 16 fundamental modes, i.e., the A1g-type vibrations ν1, ν2, ν3, ν4, ν5, and [lowercase_phi_synonym]8, the B1g vibrations ν11 and ν14, the B2g vibrations ν28, ν29, and ν30 and the antisymmetric A2g modes ν19, ν20, ν22, and ν23 as function of the excitation wavelength. The data cover the entire resonant regions of the Q- and B-bands. They were analyzed by use of a theory which describes intra- and intermolecular coupling in terms of a time-independent nonadiabatic perturbation theory [E. Unger, U. Bobinger, W. Dreybrodt, and R. Schweitzer-Stenner, J. Phys. Chem. 97, 9956 (1993)]. This approach explicitly accounts in a self-consistent way for multimode mixing with all Raman modes investigated. The vibronic coupling parameters obtained from this procedure were then used to successfully fit the vibronic side bands of the absorption spectrum and to calculate the resonance excitation profiles in absolute units. Our results show that the porphyrin macrocycle is subject to B2u-(saddling) and B1u-(ruffling) distortions which lower its symmetry to S4. Thus, evidence is provided that the porphyrin molecule maintains the nonplanar structure of its crystal phase in an organic solvent. The vibronic coupling parameters indicate a breakdown of the four-orbital model. This notion is corroborated by (ZINDO/S) calculations which reveal that significant configurational interaction occurs between the electronic transitions into |Q>- and |1B>-states and various porphyrin→porphyrin, metal→porphyrin, and porphyrin→metal transitions. The intrastate coupling parameters are used to estimate the excited electronic states’ displacements along the normal coordinates with respect to the ground state and their contributions to the reorganization energy. It turns out that the |B>-state is predominantly affected by symmetric A1g-displacements, whereas the |Q>-state is subject to A2g, B1g, and B2g displacements of its equilibrium configuration. While the former is induced by the combined effect of ruffling and saddling, the latter arises from Jahn–Teller coupling within the degenerate states. © 1997 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Background: We present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque. Results: The assembly process consisted of multiple phases: First, BACs were assembled with BAC generated sequence, then subsequently in combination with the individual overlapping WGS reads. Different assembly parameters were tested to separately optimize the performance for each BAC assembly of the BAC and WGS reads. In parallel, a second assembly was produced using only the WGS sequences and a global whole genome assembly method. The two assemblies were combined to create a more complete genome representation that retained the high quality BAC-based local assembly information, but with gaps between BACs filled in with the WGS-only assembly. Finally, the entire assembly was placed on chromosomes using the available map information. Over 90% of the assembly is now placed on chromosomes. The estimated genome size is 2.87 Gb which represents a high degree of completeness, with 95% of the available EST sequences found in assembled contigs. The quality of the assembly was evaluated by comparison to 73 finished BACs, where the draft assembly covers between 92.5 and 100% (average 98.5%) of the finished BACs. The assembly contigs and scaffolds align linearly to the finished BACs, suggesting that misassemblies are rare. Genotyping and genetic mapping of 17,482 SNPs revealed that more than 99.2% were correctly positioned within the Btau_4.0 assembly, confirming the accuracy of the assembly. Conclusion: The biological analysis of this bovine genome assembly is being published, and the sequence data is available to support future bovine research. [ABSTRACT FROM AUTHOR]

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

Objective: To investigate the changes of apoptosis and the activity of caspases 3 and 9 in bone marrow hematopoietic progenitor cells in myelodysplastic syndromes (MDS)., Methods: Bone marrow hematopoietic progenitor cells (including both CD(34)(+) and CD(34)(-) cells) were collected by negative selection in 34 patients with MDS. Apoptosis was measured with Annexin V assay and activities of caspases 3 and 9 by spectrophotometer., Results: 1. Apoptosis was significantly increased in MDS-RA (39.5%, P < 0.01) and MDS-RAEB (31.0%, P < 0.05), but was not different statistically in MDS-RAEBt/AML (18.8%) compared with that of control. 2. Activities of caspases 3 and 9 increased 45 and 20 fold in MDS-RA, increased 14 and 2 fold in MDS-RAEB, respectively and was not increased in MDS-RAEBt/AML compared with that of control. 3. Apoptosis and activities of caspases 3 and 9 reduced in 3 cases of MDS-RAEB group who progressed into AML., Conclusion: Increased activities of caspases 3 and 9 may be one of causes of excessive apoptosis in MDS. With progress to AML, activities of caspases 3 and 9 and apoptosis reduced. Reduced activity of caspase 9 may result in apoptosis "escape" and progression into AML.