Efficient, Distributed and Interactive Neuroimaging Data Analysis Using the LONI Pipeline.

The LONI Pipeline is a graphical environment for construction, validation and execution of advanced neuroimaging data analysis protocols (Rex et al., 2003). It enables automated data format conversion, allows Grid utilization, facilitates data provenance, and provides a significant library of computational tools. There are two main advantages of the LONI Pipeline over other graphical analysis workflow architectures. It is built as a distributed Grid computing environment and permits efficient tool integration, protocol validation and broad resource distribution. To integrate existing data and computational tools within the LONI Pipeline environment, no modification of the resources themselves is required. The LONI Pipeline provides several types of process submissions based on the underlying server hardware infrastructure. Only workflow instructions and references to data, executable scripts and binary instructions are stored within the LONI Pipeline environment. This makes it portable, computationally efficient, distributed and independent of the individual binary processes involved in pipeline data-analysis workflows. We have expanded the LONI Pipeline (V.4.2) to include server-to-server (peer-to-peer) communication and a 3-tier failover infrastructure (Grid hardware, Sun Grid Engine/Distributed Resource Management Application API middleware, and the Pipeline server). Additionally, the LONI Pipeline provides three layers of background-server executions for all users/sites/systems. These new LONI Pipeline features facilitate resource-interoperability, decentralized computing, construction and validation of efficient and robust neuroimaging data-analysis workflows. Using brain imaging data from the Alzheimer's Disease Neuroimaging Initiative (Mueller et al., 2005), we demonstrate integration of disparate resources, graphical construction of complex neuroimaging analysis protocols and distributed parallel computing. The LONI Pipeline, its features, specifications, documentation and usage are available online (http://Pipeline.loni.ucla.edu).

Amino acid sequences of cytochromes c2 and c' from the moderately halophilic purple phototrophic bacterium Rhodospirillum salexigens.

Rhodospirillum salexigens is a moderately halophilic purple phototrophic bacterium which grows optimally in 8% NaCl. The amino acid sequences of the two principal soluble cytochromes c have been determined. One of these is a cytochrome c2, similar in size to mitochondrial cytochrome c. While clearly of the same sequence class as mitochondrial cytochrome c and the proteins from several other Gram-negative bacteria, it does not show particular affinity to any already known sequence in terms of the percentage sequence identity. The other protein is a cytochrome c', but is also a divergent member of this widespread group. The lack of appreciable sequence identity to other species is probably due to a limit of divergence which has been reached for the majority of purple bacterial species. However, the numbers of insertions and deletions and their locations in cytochromes c2 and c' suggest that R salexigens may be related to Rhodospirillum molischianum. Like other electron transport proteins from halophiles, both of these cytochromes are notable for their high content of arginine as compared with lysine and both are acidic. However, they do not show any particular sequence homology to electron transport proteins that have been characterized from the extremely halophilic phototrophes of the genus Ectothiorhodospira. Thus, it appears that adaptation to halophilic habitats has independently occurred more than once in purple bacteria.

Amino acid sequences of two high-potential iron sulfur proteins (HiPIPs) from the moderately halophilic purple phototrophic bacterium Ectothiorhodospira vacuolata.

There are two equally abundant high-potential iron sulfur protein (HiPIP) isozymes present in the purple sulfur bacterium Ectothiorhodospira vacuolata. We have determined the amino acid sequences, which contain 71 and 72 residues. The two HiPIPs can be aligned without any internal insertions or deletions and are 65% identical to one another. The E. vacuolata HiPIPs are most similar to the HiPIP isozymes from Ectothiorhodospira halophila (32-36% identity) and require at least one internal gap for alignment. Other HiPIPs require greater numbers of insertions and deletions for alignment with those of E. vacuolata and E. halophila, and the percentage similarities are slightly smaller (19-40% identity). The E. vacuolata HiPIP isozymes appear to be slightly closer to other species than are the E. halophila isozymes. The E. vacuolata and E. halophila HiPIPs also show slightly greater similarity to the five species of Chromatiaceae, which have been studied, and less similarity to the non-sulfur purple species. These results are in agreement with other studies, which indicate that the two purple sulfur bacterial families, Ectothiorhodospiraceae and Chromatiaceae, are more closely related to one another than to the Rhodospirillaceae.

Amino acid sequence of a high redox potential ferredoxin (HiPIP) from the purple phototrophic bacterium Rhodopila globiformis, which has the highest known redox potential of its class.

Rhodopila globiformis HiPIP has a redox potential (ca. 450 mV) that is 100 mV higher than any other known iron-sulfur protein. The amino acid sequence contains 57 residues and can be aligned with that of Thiobacillus ferrooxidans without any insertions or deletions and is 51% identical. Rp. globiformis HiPIP is also similar to that of Rhodocyclus tenuis, but six- and two-residue gaps must be postulated and there is only 37% identity. Most of the amino acid residues near the iron-sulfur cluster are similar in these two species based on inspection of the three-dimensional structure of Rc. tenuis HiPIP. The reason for the higher redox potential may be a more hydrophilic environment of the Rp. globiformis HiPIP iron-sulfur cluster due to the above two deletions and to substitution of Ser 32 for Gly. Rp. globiformis is unusual in that it has a cytochrome c2 in addition to the HiPIP, and it too has a very high redox potential. These results suggest that the cytochrome c2 and HiPIP may function interchangeably and that the species normally resides in a very high potential environment, although it is not known to grow aerobically in the dark.

Amino acid sequences of cytochromes c-551 from the halophilic purple phototrophic bacteria, Ectothiorhodospira halophila and E. halochloris.

The cytochromes c-551 from Ectothiorhodospira halophila and E. halochloris contain 78 and 79 residues, respectively. The sequences can be aligned without the need to postulate any internal deletions or insertions to give 63% identity. They are apparently distantly related to the class I cytochromes c, based on the location of the heme attachment site near the N-terminus and the sixth ligand methionine near the C-terminus. Alignment with cytochromes c5 from Azotobacter and Pseudomonas, with cytochromes c6 from cyanobacteria and algae, and with cytochromes c-555 from the green phototrophic bacteria suggests that residues which occupy important positions in the three-dimensional structures of these proteins have their equivalents in the Ectothiorhodospira cytochromes c-551, but the levels of overall identity are very low, around 30%. Although the Ectothiorhodospira cytochromes c-551 are apparently distantly related to the above, they should be regarded as representative of a new subclass of type I bacterial cytochromes c. Homologs of all of the cytochromes c normally found in Pseudomonas and Azotobacter have now been found in one or more purple bacterial species. Among these, cytochrome c5 homologs are the most widely occurring in purple, green, and cyanobacteria. For the first time, all families of phototrophic bacteria plus Pseudomonas can be related to one another at the molecular level.

Percutaneous transluminal coronary angioplasty of a right coronary artery arising from the left main coronary artery.

Angioplasty of anomalous coronary arteries presents unique technical challenges. Correct guiding catheter selection is important to ensure adequate access to the anomalous vessel and to provide support to cross the lesion. A case of successful PTCA of a lesion in an anomalous right coronary artery arising from the left main coronary artery is presented.

International workshop on non-mitochondrial cytochromes c. A short foreword with some history.

A brief description of the informal workshop on non-mitochondrial cytochromes c is given. The organization of the meeting, the personnel participating and the scope of research effort are discussed. A brief historical account is included to place the Symposium reports in context.

Amino acid sequences of Euglena viridis ferredoxin and cytochromes c.

The Order Euglenida comprises many species and perhaps 40 genera, but almost all biochemical and genetic studies have been limited to a single species. Euglena gracilis, because of its ease of growth in the laboratory. Sequence studies of chloroplast and mitochondrial proteins from E. gracilis show that they have diverged widely from other eukaryotic lines. In the present paper we report the sequences of three proteins from another euglenoid, Euglena viridis, using material isolated from a natural bloom. The mitochondrial cytochrome c shows more than 90% sequence identity with that from E. gracilis, and contains the same characteristic features. The chloroplast cytochrome c6 has diverged to a greater extent and shows only 77% identity. The chloroplast ferredoxin from E. viridis is similar in sequence to those of cyanobacteria and algal chloroplasts, with sequence identities of up to 75%. Details of the purification, analysis and sequence determination experiments on the peptides have been deposited as Supplementary Publication SUP 50163 (32 pages) at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1991) 273, 5.

Preoperative left and right ventricular performance in combined aortic and mitral regurgitation and comparison with isolated aortic or mitral regurgitation.

Left and right ventricular performance characteristics in operative candidates with combined aortic and mitral regurgitation (AR/MR) have not been well defined. Therefore, we determined radionuclide cineangiographic ejection fractions, as well as echocardiographic and hemodynamic parameters, in 8 symptomatic patients undergoing double-valve replacement with pure, severe AR/MR. In order to gain insight into the basis for the poor postoperative survival in patients with this intrinsically biventricular disease, we compared these results with those of 29 symptomatic patients with isolated AR and with 18 symptomatic patients with isolated MR, all also undergoing valve replacement. Before operation, patients with AR/MR had significantly lower left ventricular (LV) ejection fraction than patients with MR (rest, 40 +/- 9% vs 52 +/- 10%, p less than 0.025; exercise, 35 +/- 12% vs 54 +/- 12%, p less than 0.005) and tended to have lower LV ejection fraction than patients with AR alone (rest, 40 +/- 9% vs 45 +/- 12%, difference not significant; exercise, 35 +/- 12% vs 39 +/- 11%, difference not significant); right ventricular (RV) ejection fraction was lower in AR/MR than in AR (p less than 0.01), and tended to be lower than in MR (difference not significant). At average postoperative follow-up of 72 to 76 months (survivors in each group), symptomatic patients with AR/MR had significantly poorer survival than symptomatic patients with isolated MR (p less than 0.05) and were more likely to have persistent symptoms than patients with AR (p less than 0.05). These findings suggest that symptomatic patients with AR/MR have poorer LV and RV performance than similarly symptomatic operative candidates with AR or MR alone.(ABSTRACT TRUNCATED AT 250 WORDS)

Current footwear technology.

This article is an in-depth review of footwear as it exists today. An historical perspective of the development of athletic shoegear is presented. A discussion of the development, construction, and features of athletic shoegear is included. Emphasis is placed on using these shoes as therapeutic modalities.

Amino acid sequences of cytochrome c-554(548) and cytochrome c' from a halophilic denitrifying bacterium of the genus Paracoccus.

The amino acid sequences of the cytochromes c-554(548) and c' from the moderately halophilic bacterium Paracoccus sp., I.A.M. 203 (= A.T.C.C. 12084, N.C.I.B. 8669) have been determined. Cytochrome c-554(548) consists of a single polypeptide chain of 83 residues, and dimerizes strongly. The most similar protein of known sequence is the N-terminal half of the dihaem cytochrome c4, and other related proteins include the cytochrome c-554(547) of Thiobacillus neapolitanus and the cytochrome c-553 of Desulfovibrio vulgaris. Cytochrome c', which has a single polypeptide chain of 132 residues, is similar in sequence to cytochromes c' from phototrophic and denitrifying bacteria, but only shows about 36% sequence identity to the most similar protein of known sequence. Both of the Paracoccus proteins have a considerable excess of acidic amino acid side chains over basic ones, and a higher proportion of their basic amino acids is arginine than is usual in cytochromes c. Both these characteristics seem to be adaptations to increase the stability of the proteins in an environment of high ionic strength. Detailed evidence for the amino acid sequences of the proteins has been deposited as Supplementary Publication 50140 (24 pp.) at the British Library (Lending Division), Boston Spa, Yorkshire LS23 7BQ, U.K. from which copies are available on prepayment.

The amino acid sequence of the cytochrome c2 from the phototrophic bacterium Rhodopseudomonas globiformis.

The amino acid sequence of the principal soluble cytochrome c from the phototrophic acidophilic bacterium Rhodopseudomonas (or Rhodopila) globiformis was determined. By the criteria of percentage sequence identity and fewness of internal insertions and deletions it is more similar in sequence to some mitochondrial cytochromes c than to any known bacterial cytochrome. The organism does not have any properties that commend it as being particularly similar to postulated prokaryotic precursors of the mitochondrion. We consider that the relatively high degree of sequence similarity is an instance of convergence, and is an example of the limitations that are imposed on attempts to deduce distant evolutionary relationships from sequence information. Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50136 (12 pages) at the British Library Lending Division, Boston Spa, West Yorkshire LS23 7BQ, U.K., from whom copies are available on prepayment [see Biochem. J. (1987) 241, 5].

The amino acid sequence of cytochrome c-555 from the methane-oxidizing bacterium Methylococcus capsulatus.

The amino acid sequence of the cytochrome c-555 from the obligate methanotroph Methylococcus capsulatus strain Bath (N.C.I.B. 11132) was determined. It is a single polypeptide chain of 96 residues, binding a haem group through the cysteine residues at positions 19 and 22, and the only methionine residue is a position 59. The sequence does not closely resemble that of any other cytochrome c that has yet been characterized. Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50131 (12 pages) at the British Library Lending Division, Boston Spa, West Yorkshire LS23 7BQ, U.K., from whom copies are available on prepayment.

Evidence against use of bacterial amino acid sequence data for construction of all-inclusive phylogenetic trees.

It has been proposed that phylogenetic trees, intended to show divergence of eukaryotic protein and nucleic acid sequences, be extended to include those from bacteria. However, we have compared the amino acid sequences of 18 of the most divergent mitochondrial cytochromes c with those of 18 bacterial cytochromes c2 and have found that the average percentage difference between these mitochondrial cytochromes c and cytochromes c2 was not significantly greater than that among the cytochromes c2 alone. The large discontinuities in physical-chemical properties recognized between the prokaryote and eukaryote cytochromes render it highly improbable that members of the two classes should be no more different from one another than members of either class alone, assuming that sequence differences can accurately reveal evolutionary divergence. Instead, we propose that divergent amino acid sequences approach a limit of change considerably less than for comparison of random sequences. This limit of change presumably is determined by the structure/function relationship. When two homologous protein sequences have reached such a limit, convergence or back-mutations and parallel mutations become as frequent as divergent mutations. As two diverging proteins approach this steady-state condition, sequence differences no longer reflect the numbers of mutations resulting in amino acid substitution and therefore species cannot be positioned on a phylogenetic tree. Insertions and deletions are less reversible than are amino acid substitutions and, provided they are well-documented, might be more reliable indicators of bacterial relationships. Nevertheless, we suggest that data available on bacterial protein sequences do not permit construction of all-inclusive phylogenetic trees. Comparisons of protein and rRNA trees suggest that similar restrictions apply to use of rRNA sequence data.

Amino acid sequence of high-redox-potential ferredoxin (HiPIP) isozymes from the extremely halophilic purple phototrophic bacterium, Ectothiorhodospira halophila.

The amino acid sequences of high-redox-potential ferredoxin (HiPIP) isozymes from Ectothiorhodospira halophila have been determined. These are: isozyme I, EPRAEDGHAHDYVNEAADPSHGRYQEGQLCENCAFWGEAVQDGWGRCTHPDFDEVLVKAEGWCSVYAPA S, and isozyme II, GLPDGVEDLPKAEDDHAHDYVNDAADTDHARFQEGQLCENCQFWVDYVNGWGYCQHPDFTDVLVRGEGW CSVYAPA. Isozyme II is the major form of HiPIP produced by the bacterium (65-80%) and is the most acidic of the known HiPIPs. The two isozymes are 72% identical to one another and require only a single residue deletion for alignment. Comparison of these HiPIPs with seven previously determined sequences revealed only 27% average identity. Both E. halophila HiPIP isozymes are likely to be functional since their sequences are equally distant from those of other species. The E. halophila HiPIP sequences show that H-bonding patterns recognized in Chromatium vinosum HiPIP are likely to be conserved and therefore cannot explain the unusually low redox potentials which have been reported.