A study of structural determinants in the interleukin-1 fold

The structures of interleukin-1ß, basic fibroblastgrowth factor and Erythrina trypsin inhibitor have been analysedin order to determine whether the hydrophobic core remains conserved,even when the structures have extremely low sequence similarities.We find that there are significant differences in the way eachprotein achieves a satisfactory arrangement of core residuesand that positions which contribute to the core of one structureare not guaranteed to contribute to the integrity of another.Furthermore, the side-chain packing arrangements of these coreresidues vary significantly between the three structures. Duringthis analysis the side-chain rotamers for three independentlydetermined interleukin-1ß structures were also compared.It was found that although buried residues are generally inagreement the remaining residues frequently occupy differentrotamers in the three structures. This suggests that althoughmeaningful studies are possible for buried side-chains the resultsobtained from equivalent analyses of accessible residues shouldbe treated with caution. These results are discussed with specificreference to the optimization of side-chain packing in proteinsof known structure.     

Comparing Dot and Landscape Spatializations for Visual Memory Differences

Spatialization displays use a geographic metaphor to arrange non-spatial data. For example, spatializations are commonly applied to document collections so that document themes appear as geographic features such as hills. Many common spatialization interfaces use a 3-D landscape metaphor to present data. However, it is not clear whether 3-D spatializations afford improved speed and accuracy for user tasks compared to similar 2-D spatializations. We describe a user study comparing users' ability to remember dot displays, 2-D landscapes, and 3-D landscapes for two different data densities (500 vs. 1000 points). Participants' visual memory was statistically more accurate when viewing dot displays and 3-D landscapes compared to 2-D landscapes. Furthermore, accuracy remembering a spatialization was significantly better overall for denser spatializations. Theseresults are of benefit to visualization designers who are contemplating the best ways to present data using spatialization techniques.     

eSeeTrack--visualizing sequential fixation patterns

We introduce eSeeTrack, an eye-tracking visualization prototype that facilitates exploration and comparison of sequential gaze orderings in a static or a dynamic scene. It extends current eye-tracking data visualizations by extracting patterns of sequential gaze orderings, displaying these patterns in a way that does not depend on the number of fixations on a scene, and enabling users to compare patterns from two or more sets of eye-gaze data. Extracting such patterns was very difficult with previous visualization techniques. eSeeTrack combines a timeline and a tree-structured visual representation to embody three aspects of eye-tracking data that users are interested in: duration, frequency and orderings of fixations. We demonstrate the usefulness of eSeeTrack via two case studies on surgical simulation and retail store chain data. We found that eSeeTrack allows ordering of fixations to be rapidly queried, explored and compared. Furthermore, our tool provides an effective and efficient mechanism to determine pattern outliers. This approach can be effective for behavior analysis in a variety of domains that are described at the end of this paper.     

Application of high-throughput computing in bioinformatics

We describe the challenges faced when developing a Linux/PC-based cluster to apply bioinformatics algorithms to the rapidly increasing raw genomics data available. The calculations, which take around two months to complete, result in a powerful resource that can be used for data mining--most obviously for the human genome. Our current infrastructure consists of a 1314 node cluster with 1734 processors supporting both production and research. This paper highlights the problems in achieving high data throughput with such systems and shows that raw computer power is only one component of a complex problem.     

CATH--a hierarchic classification of protein domain structures

BACKGROUND: Protein evolution gives rise to families of structurally related proteins, within which sequence identities can be extremely low. As a result, structure-based classifications can be effective at identifying unanticipated relationships in known structures and in optimal cases function can also be assigned. The ever increasing number of known protein structures is too large to classify all proteins manually, therefore, automatic methods are needed for fast evaluation of protein structures. RESULTS: We present a semi-automatic procedure for deriving a novel hierarchical classification of protein domain structures (CATH). The four main levels of our classification are protein class (C), architecture (A), topology (T) and homologous superfamily (H). Class is the simplest level, and it essentially describes the secondary structure composition of each domain. In contrast, architecture summarises the shape revealed by the orientations of the secondary structure units, such as barrels and sandwiches. At the topology level, sequential connectivity is considered, such that members of the same architecture might have quite different topologies. When structures belonging to the same T-level have suitably high similarities combined with similar functions, the proteins are assumed to be evolutionarily related and put into the same homologous superfamily. CONCLUSIONS: Analysis of the structural families generated by CATH reveals the prominent features of protein structure space. We find that nearly a third of the homologous superfamilies (H-levels) belong to ten major T-levels, which we call superfolds, and furthermore that nearly two-thirds of these H-levels cluster into nine simple architectures. A database of well-characterised protein structure families, such as CATH, will facilitate the assignment of structure-function/evolution relationships to both known and newly determined protein structures.     

Suppression of inflammatory neurotoxins by highly active antiretroviral therapy in human immunodeficiency virus-associated dementia

The development in culture of 1-cell hamster embryos prior to the completion of fertilization is not well understood. In this study it was observed that culture for only 6 h of these early 1-cell embryos collected before pronuclei formation (3 h post-egg activation; PEA) significantly increased intracellular free calcium levels (194.3 +/- 3.1 nM) compared to levels in similarly aged 1-cell embryos collected from the oviduct at 9 h PEA, after pronuclei formation is complete (134.2 +/- 6.8 nM). Not only was the developmental competence of cultured 3-h PEA embryos with elevated intracellular free calcium levels compromised as compared with that of embryos collected from the oviduct at 9 h PEA; these embryos also had impaired cytoplasmic mitochondrial distribution (ratio of 0.62 +/- 0. 06 for cultured embryos compared to 0.44 +/- 0.04 for in vivo-developed embryos) and decreased lactate metabolism (2.93 +/- 0. 22 pmol/embryo per 3 h for cultured embryos compared to 5.37 +/- 0. 36 for in vivo-developed embryos). This impairment in mitochondrial distribution and function and reduced development in culture by 3-h PEA embryos appears related to the ability to regulate intracellular calcium homeostasis. Intracellular free calcium levels were reduced by culture with increased medium magnesium concentrations, calcium channel inhibitors nifedipine or verapamil, or an intracellular calcium chelator. All of these treatments also stimulated development of 3-h PEA embryos to the morula/blastocyst stages and prevented impairment in mitochondrial organization and function. Conversely, culture with low medium magnesium and high calcium concentrations that increased intracellular free calcium levels resulted in low development and reduced mitochondrial function. Therefore, it appears that removal of the early embryo from the oviduct results in an inability to regulate intracellular calcium levels. As increased magnesium concentrations, nifedipine, and verapamil inhibit L-gated calcium channels, it may be a loss of regulation of these channels that alters calcium homeostasis resulting in impaired developmental competence.     

Mechanisms for the transendothelial migration of HIV-1-infected monocytes into brain

HIV-1 penetration of the brain is a pivotal event in the neuropathogenesis of AIDS-associated dementia. The establishment of productive viral replication or up-regulation of adhesion molecule expression on brain microvascular endothelial cells (BMVEC) could permit entry of HIV into the central nervous system. To investigate the contribution of both, we inoculated primary human BMVEC with high titer macrophage-tropic HIV-1 or cocultured them with virus-infected monocytes. In both instances, BMVEC failed to demonstrate productive viral replication. Cell to cell contact between monocytes and microvascular endothelium resulted in E-selectin expression on BMVEC. BMVEC. cocultured with LPS-activated HIV-infected monocytes expressed even higher levels of E-selectin and vascular cell adhesion molecule-1 (VCAM-1). Transwell assays supported a role of soluble factors, from virus-infected monocytes, for the induction of adhesion molecules on BMVEC. To verify the in vivo relevance of these findings, levels of adhesion molecules were compared with those of proinflammatory cytokines and HIV-1 gene products in brain tissue of AIDS patients with or without encephalitis and HIV-seronegative controls. E-Selectin, and to a lesser degree VCAM-1, paralleled the levels of HIV-1 gene products and proinflammatory cytokines in brain tissue of subjects with encephalitis. Most importantly, an association between macrophage infiltration and increased endothelial cell adhesion molecules was observed in encephalitic brains. Monocyte binding to encephalitic brain tissue was blocked with Abs to VCAM-1 and E-selectin. These data, taken together, suggest that HIV entry into brain is, in part, a consequence of the ability of virus-infected and immune-activated monocytes to induce adhesion molecules on brain endothelium.     

Contemporary approaches to protein structure classification

In a similar manner to sequence database searching, it is also possible to compare three-dimensional protein structure. Such methods can be extremely useful because a structural similarity may represent a distant evolutionary relationship that is undetectable by sequence analysis. In this review, we summarise the most popular structure comparison methods, show how they can be used for database searching, and then describe some of the most advanced attempts to develop comprehensive protein structure classifications. With such data, it is possible to identify distant evolutionary relationships, provide libraries of unique folds for structure prediction, estimate the total number of folds that exist, and investigate the preference for certain types of structures over others.     

A new form of the Dean test for the hot- corrosion resistance of gas- turbine alloys and coatings

A new form of the Dean-type of hot corrosion test has been developed which deposits NaSO₂SOSO₄ salt and other salts either separately or in combination on the surface of test samples of gas turbine alloys and blade coatings. Control over the salt deposition is achieved with furnace tubes in a T-shape, with the salts in the cross arms and the specimens in the vertical section. The deposition rate for NaSO₂SOSO₄ could be either 8 µgcm^-2h^-1 or 14 µgcm^-2h^-1 depending on the gas flow arrangement. 8ulphidation was only achieved when the carrier gas contained SO₂/SO₃. The effectiveness of the apparatus was demonstrated by tests on coated and uncoated gas turbine alloys which showed the correct morphology for corrosion at 830-850°C. Coated alloys tested at 700°C also corroded, and to a greater extent than at 850°C.     

Silicon microsegregation and first stage graphitization in white cast irons

The distribution of silicon in a series of as-cast white irons containing up to 3.25 pct Si and from 2.39 to 3.94 pct C was studied using electron probe microanalysis. The silicon content of the proeutectic austenite dendrites is a linear function of the silicon content of the alloy. The periphery of these dendrites is richer in silicon than the core due to the rejection of the element from the cementite formed during eutectic solidification and the enrichment is most pronounced at slow rates of solidification. It was also firmly established that silicon is present in the eutectic cementite, the level increasing with solidification rate and with the silicon content of the alloy. The nonuniform distribution of silicon persisted for a large part of a graphitization anneal. The effects of the silicon in the cementite and at the austenite-cementite interface on the nucleation of graphite during first stage graphitization are discussed in terms of the thermodynamics of graphitization.