The use of alloderm as an adjunct in the closure of the bladder - Cloacal exstrophy complex.

OBJECTIVE: To decrease the incidence of vesicocutaneous fistulae (VCF), intra-pubic stitch erosion (IPE) and intrasymphyseal plate erosion (ISE) of bladder or cloacal exstrophy in patients undergoing reclosure, we sought additional bulking material to place between the posterior urethral/bladder neck and pubic closures. MATERIAL AND METHODS: In 43 patients (2005-2009) undergoing exstrophy/cloacal exstrophy closure or reclosure, we placed human acellular dermis (HAD) between the posterior urethral/bladder neck and pubic closures. The thickest piece of HAD available was placed above the urethra and bladder neck, and attached to the pelvic floor with sutures of 4-0 Vicryl prior to pubic bone apposition. RESULTS: Twenty-three were primary and 20 were reclosures. Of the 23 primary closures, 17 were classic exstrophy and six were cloacal exstrophy. Of the 20 reclosures, 17 were classic exstrophy and three were cloacal exstrophy. Thirty-four had an osteotomy and nine did not, at the time of closure. No patient experienced failure of closure, a VCF, an IPE or an ISE into the urethra after pubic apposition, or other complication related to the use of HAD. One patient had a superficial wound infection, and one had premature suprapubic tube dislodgement requiring replacement in the operating room. CONCLUSION: From the success of this novel technique in failed closures, we have begun using HAD as an adjunct in all exstrophy closures.

Mitrofanoff continent catheterizable conduits: top down or bottom up?

OBJECTIVE: During augmentation and Mitrofanoff procedures, conduits are usually implanted into the posterior bladder wall. Anatomical considerations may necessitate an anterior conduit. To compare the relative drainage efficiency in patients with posterior and anterior conduits, we studied their rates of bladder stone formation and urinary tract infection (UTI). MATERIALS AND METHODS: A retrospective chart review identified exstrophy patients who underwent augmentation and Mitrofanoff between 1991 and 2003. Patients with 3 years or greater follow-up were included. Fifty-four patients fit this criterion, with a conduit implanted anteriorly (33) or posteriorly (21). We compared rates of bladder stone formation and UTI. Stomal revisions and the status of the bladder neck were also noted. RESULTS: Stone formation and UTI rates were higher in the anterior conduits, although only UTI showed a statistically significant difference. Patient demographics were similar between the two groups, including age and sex. The rates of stomal complications and the bladder neck status were also similar. CONCLUSIONS: Patients with anterior conduits had an increased risk of UTI and bladder stone formation compared to those with posterior conduits, although this was not significant in the case of bladder stone rate. This may indicate sub-optimal bladder drainage and should be addressed with careful preoperative counseling and close follow-up.

Social identity in adolescence.

Social identity theory (SIT) was used to investigate the effects of social categorization on adolescents' intergroup behaviour. One hundred and forty-nine male adolescents aged 14-15 years made comparisons between an ingroup and an outgroup along a series of dimensions. Participants displayed consistent ingroup-favouring behaviour in their ratings: the ingroup was associated to a greater extent than the outgroup with positively valued dimensions, and to a lesser extent with negatively valued dimensions. Those participants who demonstrated the most discrimination reported highest levels of ingroup identification. The utility of applying predictions from SIT to the study of adolescence is discussed.

Social categorization, self-esteem, and the estimated musical preferences of male adolescents.

The authors investigated the intergroup processes of male adolescents within the context of social identity theory (SIT; H. Tajfel, 1978; H. Tajfel & J. C. Turner, 1979). The participants were English male adolescents (age = 14-15 years). They estimated in-group and out-group musical preferences and evaluated the in-group and out-group along a series of scales. The results showed in-group favoritism effects along the musical preference and evaluative dimensions. The participants reported greater liking for the in-group. Compared with the out-group, they associated the in-group more with positively stereotyped music and less with negatively stereotyped music. Compared with the out-group, they rated the in-group as more fun, more masculine, more sporty, less boring, less snobbish, and less weird. The participants with lower levels of self-esteem showed greater differentiation between groups and greater derogation of the out-group. The results supported the predictions of SIT and demonstrated the applicability of SIT for the study of adolescent behavior.

The lipocalin protein family: structural and sequence overview.

Lipocalins are remarkably diverse at the sequence level yet have highly conserved structures. Most lipocalins share three characteristic conserved sequence motifs - the kernel lipocalins - while others are more divergent family members - the outlier lipocalins - typically sharing only one or two. This classification is a useful tool for analysing the family, and within these large sets are smaller groups sharing much higher levels of sequence similarity. The lipocalins are also part of a larger protein superfamily: the calycins, which includes the fatty acid binding proteins, avidins, a group of metalloproteinase inhibitors, and triabin. The superfamily is characterised by a similar structure (a repeated +1 topology beta-barrel) and by the conservation of a remarkable structural signature.

Evaporative microdialysis: an effective improvement in an established method of protein crystallization.

Evaporative dialysis is a simple variant of conventional microdialysis in which the reservoir solution is allowed to evaporate slowly. The slow increase in precipitant concentration allows crystals to grow without increasing nucleation. The method is useful for proteins that have a very narrow metastable zone (the range of solution conditions under which crystals grow but nuclei do not form at an appreciable rate). The method is demonstrated with the coat protein of potato virus X.

The importance of music to adolescents.

AIMS: The study aims to determine the importance of music to adolescents in England, and investigates why they listen to and perform music. SAMPLE: A total of 2465 adolescents (1149 males; 1266 females; 50 participants did not state their sex) between 13 and 14 years of age who were attending Year 9 at one of 22 secondary schools in the North Staffordshire region of England. METHOD: A questionnaire asked participants (a) about their degree of involvement with musical activities; (b) to rate the importance of music relative to other activities; and (c) to rate the importance of several factors that might determine why they and other people of their age and sex might listen to/perform pop and classical music. RESULTS: Responses indicated that i) over 50% of respondents either played an instrument currently or had played regularly before giving up, and the sample listened to music for an average of 2.45 hours per day; ii) listening to music was preferred to other indoor activities but not to outdoor activities; iii) listening to/playing pop music has different perceived benefits to listening to/playing classical music; iv) responses to suggested reasons for listening to music could be grouped into three factors; and v) responses to suggested reasons for playing music could be grouped into four factors. CONCLUSIONS: These results indicate that music is important to adolescents, and that this is because it allows them to (a) portray an 'image' to the outside world and (b) satisfy their emotional needs.

Musical preferences during and after relaxation and exercise.

Effects of the listening context on responses to music largely have been neglected despite the prevalence of music listening in our everyday lives. This article reports 2 studies in which participants chose music of high or low arousal potential during (Experiment 1) or immediately after (Experiment 2) exercise or relaxation. In Experiment 1, participants preferred appropriate arousal-polarizing music over arousal-moderating music. In Experiment 2, participants preferred arousal-moderating music over arousal-polarizing music, such that their listening times contrasted clearly with those in the first study even though the same music and methods were used. Thus musical preferences interact with the listening situation, and participants' music selections represent an attempt to optimize their responses to that situation. When motivated to maintain a state of polarized arousal, listeners use music to achieve this; when they have no such goal, they use music to moderate arousal.

PROMISE: a database of bioinorganic motifs.

The PROMISE (prosthetic centres andmetalions in protein activesites) database aims to present comprehensive sequence, structural, functional and bibliographic information on metalloproteins and other complex proteins, with an emphasis on active site structure and function. The database is available on the WorldWide Web at http://bioinf.leeds.ac.uk/promise/

Hard alpha-keratin intermediate filament chains: substructure of the N- and C-terminal domains and the predicted structure and function of the C-terminal domains of type I and type II chains.

The quantity of sequence data now available for both Type I and Type II hard alpha-keratin IF proteins makes it possible to analyze their N- and C-terminal domains and ascertain features of likely structural and/or functional importance. The N-terminal domains of both chain types can be divided into acidic (NA) and basic (NB) subdomains, where NA is 29 and 34 residues long, respectively, for Type I and II chains and is located immediately adjacent to the end of the rod domain. NB constitutes the remainder of the N-terminal domain and is about 27 and 70 residues long for the two chain types, respectively. The glycine residue contents, however, are high in NA(I) and NB(II), but low in NA(II) and NB(I). Subdomain NB(II) contains four consecutive nonapeptide quasirepeats of the form GGGFGYRSX. The C-terminal domain of Type I chains, termed C(I), is characterized by a PCX motif repeated 10 times, 7 of them contiguously. From an analysis of the conformation of like peptides from crystal structures it has been shown that this region will probably adopt a polyproline II left-handed helical structure with three residues per turn. In contrast, the C-terminal domain of Type II hard alpha-keratin chains (known as C(II)) contains a periodic distribution of hydrophobicities that, together with other predictive techniques, allow its conformation (a twisted four-stranded antiparallel beta-sheet) to be predicted with some degree of confidence. In addition, it is possible to suggest two partners with which this domain will interact. The first is with segment L12 in the rod domain and the second is with another C(II) domain in an antiparallel neighboring molecule. The latter possibility appears most likely. In either case the aggregation would likely serve to stabilize the molecular assembly through the interaction of two beta-sheets via their apolar faces and, in so doing, would position a number of cysteine residues in external positions that would allow them to form a number of covalent disulfide bonds with other molecules.

PROMISE: a database of information on prosthetic centres and metal ions in protein active sites.

The PROMISE (Prosthetic centres andmetalions in protein activesites) database aims to gather together comprehensive sequence, structural, functional and bibliographic information on proteins which possess prosthetic centres, with an emphasis on active site structure and function. The database is available on the World Wide Web at http://bioinf.leeds.ac.uk/promise/

Bovine beta-lactoglobulin at 1.8 A resolution--still an enigmatic lipocalin.

BACKGROUND: beta-Lactoglobulin (beta-Lg) is the major whey protein in the milk of ruminants and many other mammals. Its function is not known, but it undergoes at least two pH-dependent conformational changes which may be important. Bovine beta-Lg crystallizes in several different lattices, and medium-resolution structures of orthorhombic lattice Y and trigonal lattice Z have been published. Triclinic lattice X and lattice Z crystals grow at pH values either side of the pH at which one of the pH-induced conformational changes occurs. A full understanding of the structure is needed to help explain both the conformational changes and the different denaturation behaviour of the genetic variants. RESULTS: We have redetermined the structure of beta-Lg lattice Z at 3.0 A resolution by multiple isomorphous replacement and have partially refined it (R factor = 24.8%). Using the dimer from this lattice Z structure as a search model, the triclinic crystal form grown at pH 6.5 (lattice X) has been solved by molecular replacement. Refinement of lattice X at 1.8 A resolution gave an R factor of 18.1%. The structure we have determined differs from previously published structures in several ways. CONCLUSIONS: Incorrect threading of the sequence in the published structures of beta-Lg affects four of the nine beta strands. The basic lipocalin fold of the polypeptide chain is unchanged, however. The relative orientation of the monomers in the beta-Lg dimer differs in the two lattices. On raising the pH, there is a rotation of approximately 5 degrees, which breaks a number of intersubunit hydrogen bonds. It is not yet clear, however, why the stability of the structure should depend so heavily upon the external loop around residue 64 or the beta strand with the free thiol, each of which shows genetic variation.

Liking, arousal potential, and the emotions expressed by music.

Previous research indicates that the specific emotions expressed by stimuli may be closely associated with their pleasing and arousing qualities, and this parallels psychomusicological research on the relationship between these two stimulus qualities. In light of this, the present research contends that the emotions expressed by musical stimuli are associated with their pleasing and arousing qualities. Sixty subjects rated 32 musical excerpts on 11-point scales representing the expression of eight specific emotions. Statistical analyses showed that these emotion ratings were predictable on the basis of 60 additional subjects' ratings of each excerpt in terms of 'liking' and 'arousal potential'. This indicates that ratings of liking and arousal potential are essentially similar to ratings of the specific emotions expressed by musical stimuli. These results are discussed in terms of the relationship between liking and arousal potential, and the implications that this may have for research on affective processes.

Structural features of keratin intermediate filaments.

The first step in the assembly of a keratin intermediate filament (KIF) is the formation of a type I/type II heterodimer molecule in which two chains become aligned in parallel and close axial registration to form a flexible segmented alpha-helical coiled-coil rope 46 nm long. The segments of coiled-coil are interspersed by sequences that introduce irregularities of unknown structure. Here we have modeled two of these, the link L2 and the heptad discontinuity located near the middle of segment 2B. In a model for L2, the orientation of the coiled-coil structure is turned through about 180 degrees over the eight residue stretch constituting this link segment. In contrast, the heptad discontinuity in segment 2B would seem to result in only minimal distortion of the coiled-coil rope, contrary to previous expectations. Little is known about how the neighboring molecules are aligned and packed within the assembled KIF. Crosslinking experiments with KIF have determined that two neighboring molecules are aligned anti-parallel and axially in three ways, and predict that similarly-directed molecules could be overlapped by about 1 nm. The two-dimensional surface lattice resulting from these data predicts an axial periodicity of 22.6 nm, which in fact is visible by electron microscopy of shadowed KIF. Interestingly, most of the amino acid substitutions resulting from mutations in the keratin genes found in genodermatoses are clustered in this molecular overlap region. Although we do not yet know how the rows of antiparallel molecules fold in three dimensions to form an intact KIF, certain of the observed crosslinks could also occur between nearest neighbor parallel molecules across a four-molecule strand; that is, KIF may be built from bundles or protofibrils. These insights on molecular structure and molecular packing provide new constraints on models for KIF structure.

Structural analysis and classification of lipocalins and related proteins using a profile-search method.

A three-dimensional profile method of detecting amino-acid sequences compatible with the tertiary structure of any protein has been applied to the lipocalin family of 8-stranded beta-barrels. Profiles derived from six well-resolved lipocalin crystal structures were used to search a comprehensive, non-redundant protein sequence database. Each profile identified a sub-group of lipocalin sequences although no single profile was sufficient to identify the whole family. The alpha-1-acid glycoprotein sub-family was not identified by any lipocalin profile, indicating that known sequence differences in otherwise well conserved regions of these proteins may be reflected in structural differences. The predicted similarity between the beta-lactoglobulin and alpha-2u-globulin structures was much more marked than the similarity between their sequences, and alpha-1-microglobulin sequences were found to be compatible with the structure of epididymal retinoic acid binding protein which has an additional long C-terminal helix. Proteins of unknown structure which were predicted to be compatible with the lipocalin fold include a human mucin. In cases where a large protein family of low overall sequence similarity contains a small number of known structures, this technique can be useful in determining or confirming subtle structural relationships between family members.

Coiled-coil stutter and link segments in keratin and other intermediate filament molecules: a computer modeling study.

Structural discontinuities have previously been identified in four regions of the coiled-coil rod domain structure present in intermediate filament (IF) protein molecules. These include a point at which a phase shift occurs in the heptad periodicity characteristic of the sequence of polar and apolar residues in alpha-helical coiled-coils, and three links that lack a heptad substructure. We have studied these regions by computer-based molecular modeling and comparative sequence analysis and conclude that the phasing discontinuity can be accommodated without significant distortion of the overall double-helical chain conformation; the L2 link has a similar conformation in all different types of IF molecules, a favorable conformation being one in which the two strands wrap tightly around each other; the L12 links vary in length between different IF types but contain important sequence similarities suggestive of a partial beta structure; the L1 links show larger variations in length, a lower degree of similarity, and probably diverse structures. Variations in the overall charges of the different links suggest that ionic interactions may play a significant role in filament assembly. The results also have general significance for other alpha-fibrous proteins in which either the characteristic heptad phasing undergoes a discontinuity or where a short non-coiled-coil sequence occurs within a coiled-coil rod domain structure.

Crystallization of the NADP(+)-dependent glutamate dehydrogenase from Escherichia coli.

The NADP(+)-dependent hexameric glutamate dehydrogenase from Escherichia coli has been crystallized as the apo-enzyme and also in the presence of its substrates 2-oxoglutarate, glutamate or NADP+, using either pulsed equilibrium microdialysis, or the hanging drop method of vapour diffusion. Three non-isomorphous, but related, crystal forms have been obtained, all of which belong to the orthorhombic system and are most likely to be in space group P2(1)2(1)2(1). One crystal form is grown from ammonium sulphate, includes the apoenzyme and the binary complexes with 2-oxoglutarate or NADP+, and has cell dimensions a = 157.5 A, b = 212.5 A, c = 101.0 A with a hexamer in the asymmetric unit. Crystallizations using glutamate as the precipitant produced two further crystal forms, which show significant changes in the b and c cell dimensions with respect to the apo-enzyme crystals, with parameters a = 160.0 A, b = 217.5 A c = 92.4 A and a = 160.0 A, b = 223.0 A c = 92.4 A, respectively. X-ray diffraction photographs taken with synchrotron radiation show measurable reflections to beyond 3.0 A resolution.

Structure and sequence relationships in the lipocalins and related proteins.

The lipocalins and fatty acid-binding proteins (FABPs) are two recently identified protein families that both function by binding small hydrophobic molecules. We have sought to clarify relationships within and between these two groups through an analysis of both structure and sequence. Within a similar overall folding pattern, we find large parts of the lipocalin and FABP structures to be quantitatively equivalent. The three largest structurally conserved regions within the lipocalin common core correspond to characteristic sequence motifs that we have used to determine the constitution of this family using an iterative sequence analysis procedure. This afforded a new interpretation of the family, which highlighted the difficulties of determining a comprehensive and coherent classification of the lipocalins. The first of the three conserved sequence motifs is also common to the FABPs and corresponds to a conserved structural element characteristic of both families. Similarities of structure and sequence within the two families suggests that they form part of a larger "structural superfamily"; we have christened this overall group the calycins to reflect the cup-shaped structure of its members.