The proteome: structure, function and evolution.

This paper reports two studies to model the inter-relationships between protein sequence, structure and function. First, an automated pipeline to provide a structural annotation of proteomes in the major genomes is described. The results are stored in a database at Imperial College, London (3D-GENOMICS) that can be accessed at www.

Energetics of outer membrane phospholipase A (OMPLA) dimerization.

Outer membrane phospholipase A (OMPLA) is a widely conserved transmembrane enzyme found in Gram-negative bacteria, and it is implicated in the virulence of a number of pathogenic organisms. The regulation of the protein's phospholipase activity is not well understood despite the existence of a number of high resolution structures. Previous biochemical studies have demonstrated that dimerization of OMPLA is a prerequisite for its phospholipase activity, and it has been shown in vitro that this dimerization is dependent on calcium and substrate binding.

A comparative evaluation of two head and neck immobilization devices using electronic portal imaging.

A study was performed to compare the positioning reproducibility and the cost efficiency for two head and neck immobilization devices: the Uvex (Uvex Safety, Smithfield, USA) plastic mask system and the Finesse Frame with Ultraplast System (PLANET Medical, Svendborg, Denmark). 20 patients treated with 3D conformal radiation therapy for head and neck cancers were randomly selected (10 for each of the two different immobilization systems) and electronic portal images acquired during their course of treatment were saved and used in this study. The anatomical landmark coordinates and their shifts in the anteroposterior (AP) and craniocaudal (CC) directions with respect to the digitized simulator films for lateral fields were analysed using an in-house developed portal image registration system.

Alternate interfaces may mediate homomeric and heteromeric assembly in the transmembrane domains of SNARE proteins.

The fusion of a vesicle to a target membrane is mediated by temporally and spatially regulated interactions within a set of evolutionarily conserved proteins. Integral to proper fusion is the interaction between proteins originating on both vesicle and target membranes to form a protein bridge between the two membranes, known as the SNARE complex. This protein complex includes the single-pass transmembrane helix proteins: syntaxin and synaptobrevin.

Effects of prelinguistic communication levels on initiation and repair of communication in children with disabilities.

Purpose: This study examined the effects of expressive and receptive language levels on initiated and repaired communication acts by prelinguistic children with developmental disabilities.

Method: In this descriptive study, participants were 45 children between the ages of 3 and 6 years who had severe delays in expressive communication. Some children communicated with 12 or fewer spoken words; others communicated exclusively with gestures and vocalizations.

Posttraumatic bile leaks: role of diagnostic imaging and impact on patient outcome.

The aim of this study was to evaluate the impact of bile leaks on patient morbidity and hospital course following blunt and penetrating liver trauma. Forty patients who underwent hepatobiliary scintigraphy after trauma were included. Scintigraphic results were classified as follows: free intraperitoneal bile leak, contained bile leak, and no bile leak.

Effect of Lactobacillus GG on intestinal integrity in Malawian children at risk of tropical enteropathy.

Background: Tropical enteropathy is an asymptomatic villous atrophy of the small bowel that is prevalent in the developing world and is associated with altered intestinal function and integrity. The histology of tropical enteropathy resembles that seen in small-bowel bacterial overgrowth.

Objective: This study tested the hypothesis that treatment of 3-5-y-old Malawian children with the probiotic Lactobacillus GG would improve their intestinal function and integrity.

Statistical analysis of data from studies on experimental autoimmune encephalomyelitis.

Research in multiple sclerosis often employs animal models of the disease, especially experimental autoimmune encephalomyelitis (EAE) in rodents. The statistical analysis procedures chosen for these studies are often suboptimal, either because of violations of the assumptions of the procedure or because the analysis selected is inappropriate for the research question. In this paper, we discuss the types of research questions frequently asked in EAE studies and suggest appropriate and useful research designs and statistical methods that will optimize the information contained within the data.

Computational analysis in vitro: dynamics and plasticity of a neuro-robotic system.

When the brain interacts with the environment it constantly adapts by representing the environment in a form that is called an internal model. The neurobiological basis for internal models is provided by the connectivity and the dynamical properties of neurons. Thus, the interactions between neural tissues and external devices provide a fundamental means for investigating the connectivity and dynamical properties of neural populations.

Changes in bone mineral density in survivors of childhood acute lymphoblastic leukemia.

Background: There is little information about factors modulating bone mineral density (BMD) in survivors of childhood acute lymphoblastic leukemia (ALL).

Procedure: We analyzed data from 57 survivors (26 male, 52 Caucasian) who underwent two serial quantitative computed tomography (QCT) studies of BMD. Using multiple linear regression, we evaluated the association of BMD change with demographic variables, treatment history, hormone therapy, exercise, and tobacco and alcohol use.

Quantifying immunohistochemical staining of phospho-eIF2alpha, heme oxygenase-2 and NADPH cytochrome P450 reductase in oligodendrocytes during experimental autoimmune encephalomyelitis.

As a consequence of inflammation associated with multiple sclerosis and its animal model, experimental autoimmune encephalomyelitis (EAE), stress responses are induced in many cells within the CNS, however, those that occur within the primary pathological target, the oligodendrocyte, are not fully established. Recently, we found that phosphorylated eukaryotic initiation factor-2alpha (eIF2alpha), an inhibitor of protein translation associated with the stress response, is expressed in a greater number of oligodendrocytes in EAE animals compared to controls. However, since numerous oligodendrocytes in control animals also expressed phospho-eIF2alpha, a method was developed to detect expression levels within oligodendrocytes that did not rely on the number of oligodendrocytes that were stained.

Quantitative trait loci that control dengue-2 virus dissemination in the mosquito Aedes aegypti.

The mosquito Aedes aegypti is the most important vector of yellow fever and dengue fever flaviviruses. Ae. aegypti eradication campaigns have not been sustainable and there are no effective vaccines for dengue viruses.

The transmembrane domains of ErbB receptors do not dimerize strongly in micelles.

The epidermal growth factor receptors (erbB) constitute an important class of single pass transmembrane receptors involved in the transduction of signals important for cell proliferation and differentiation. Receptor association is a key event in the signal transduction process, but the molecular basis of this interaction is not fully understood. Previous biochemical and genetic studies have suggested that the single transmembrane helices of these receptor proteins might play a role in stabilizing the receptor complexes.

The GxxxG-containing transmembrane domain of the CCK4 oncogene does not encode preferential self-interactions.

The recently cloned colon carcinoma kinase 4 (CCK4) oncogene contains an evolutionarily conserved GxxxG motif in its single transmembrane domain (TMD). It has previously been suggested that this pairwise glycine motif may provide a strong driving force for transmembrane helix-helix interactions. Since CCK4 is thought to represent a new member of the receptor tyrosine kinase family, interactions between the TMDs may be important in receptor self-association and activation of signal transduction pathways.

Virtual outreach: a randomised controlled trial and economic evaluation of joint teleconferenced medical consultations.

Objectives: To test the hypotheses that virtual outreach would reduce offers of hospital follow-up appointments and reduce numbers of medical interventions and investigations, reduce numbers of contacts with the health care system, have a positive impact on patient satisfaction and enablement, and lead to improvements in patient health status. To perform an economic evaluation of virtual outreach.

Design: A randomised controlled trial comparing joint teleconsultations between GPs, specialists and patients with standard outpatient referral.

Complex interactions at the helix-helix interface stabilize the glycophorin A transmembrane dimer.

To explore the residue interactions in the glycophorin A dimerization motif, an alanine scan double mutant analysis at the helix-helix interface was carried out. These data reveal a combination of additive and coupled effects. The majority of the double mutants are found to be equally or slightly more stable than would be predicted by the sum of the energetic cost of the single-point mutants.

Blunt trauma of the pancreas and biliary tract: a multimodality imaging approach to diagnosis.

Injuries of the pancreas, gallbladder, and bile ducts due to blunt trauma are relatively uncommon and difficult to detect but are associated with high morbidity and mortality, especially if diagnosis is delayed. Accurate and early diagnosis is imperative, and imaging plays a key role in detection. Knowledge of the mechanisms of injury, the types of injuries, and the roles of various imaging modalities is essential for prompt and accurate diagnosis.

Binding of polyubiquitin chains to ubiquitin-associated (UBA) domains of HHR23A.

Ubiquitin-associated (UBA) domains are small protein domains that occur in the context of larger proteins and are likely to function as inter- and intramolecular communication elements in ubiquitin/polyubiquitin signaling. Although monoubiquitin/UBA complexes are well characterized, much less is known about UBA/polyubiquitin complexes, even though polyubiquitin chains are believed to be biologically relevant ligands of many UBA domain proteins. Here, we report the results of a quantitative study of the interaction of K48-linked polyubiquitin chains with UBA domains of the DNA repair/proteolysis protein HHR23A, using surface plasmon resonance and other approaches.

Media for studies of partially aligned states.

Measurement of residual dipolar couplings for proteins in nuclear magnetic resonance (NMR) requires a degree of molecular alignment. This may be achieved through the use of liquid crystals or compressed hydrated gels. Several media have been described in the literature, and this chapter describes five of the most commonly used systems.

Sequence context modulates the stability of a GxxxG-mediated transmembrane helix-helix dimer.

To quantify the relationship between sequence and transmembrane dimer stability, a systematic mutagenesis and thermodynamic study of the protein-protein interaction residues in the glycophorin A transmembrane helix-helix dimer was carried out. The results demonstrate that the glycophorin A transmembrane sequence dimerizes when its GxxxG motif is abolished by mutation to large aliphatic residues, suggesting that the sequence encodes an intrinsic propensity to self-associate independent of a GxxxG motif. In the presence of an intact GxxxG motif, the glycophorin A dimer stability can be modulated over a span of -0.

Clustering of protein domains in the human genome.

We present a systematic study of the clustering of genes within the human genome based on homology inferred from both sequence and structural similarity. The 3D-Genomics automated proteome annotation pipeline () was utilised to infer homology for each protein domain in the genome, for the 26 superfamilies most highly represented in the Structural Classification Of Proteins (SCOP) database. This approach enabled us to identify homologues that could not be detected by sequence-based methods alone.

Prelinguistic predictors of language growth in children with developmental disabilities.

This study followed 18 children with developmental disabilities, whose chronological ages were between 3 years and 6 years at the start of the study, over a 2-year period. At initial observation, children communicated primarily through prelinguistic gestures, vocalizations, and single-word utterances. Children's language skills were measured every 6 months with the Sequenced Inventory of Communication Development-Revised (D.

Equivalence of high-virulence clonotypes of serotype III group B Streptococcus agalactiae (GBS).

Analysis of growth characteristics, multilocus enzyme electrophoresis, restriction digest pattern (RDP) typing and multilocus sequence typing have identified clonotypes of serotype III group B Streptococcus agalactiae (GBS) associated with invasive infection in neonates. This study sought to unify phenotypic and genotypic classifications of type III GBS strains associated with increased virulence in newborns. High-virulence clonotype (HVC) strains possessed the translation initiation factor 2 (infB) C allele, found in RDP type III-3 strains, and hybridized with the RDP type III-3-specific probe AA3.