Report on the development of the New South Wales Child Health Survey 2001.
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Child↗
Biomedical subjects
D Baker
Publications and source records attributed to D Baker.
The early effect of lipid-lowering treatment on carotid and femoral intima media thickness (IMT).
OBJECTIVES: an increased intima media thickness (IMT) is an early indicator of the atherosclerotic process. We investigated the early effect of atorvastatin on the common carotid artery (CCA) and common femoral artery (CFA) IMT. METHODS: the IMT was measured in the CCA and the CFA of hyperlipidaemic patients referred with peripheral vascular disease. The measurements were performed using an automated radio frequency IMT technique pre-treatment and at 4 and 8 weeks post-treatment with 20 mg/day atorvastatin. RESULTS: patients (14 men; 11 women), median age 69 years (range: 48-81) had a CCA-IMT mean (SD) of 0.79 (0.21) mm pre-treatment, 0.75 (0.22) mm after 4 weeks, and 0.64 (0.15) mm after 8 weeks. The ANOVA test was significant (p=0.024) for the CCA-IMT trend. The corresponding CFA-IMT readings were 0.83 (0.13) mm, 0.80 (0.09) mm and 0.69 (0.14) mm (p=0.0003). After 8 weeks of treatment there was a significant reduction in total cholesterol 6.0 (0.3) to 4.3 (0.8) mmol/l, p=0.0004 and low-density lipoprotein cholesterol 3.7 (0.2) to 2.2 (0.5), p=0.0001. There was a significant decrease in median serum creatinine levels after 8 weeks treatment: 87 micromol/l (range 67-114) to 84 micromol/l (range: 64-112), p=0.007. CONCLUSIONS: cholesterol-lowering with atorvastatin 20 mg/day leads to a decrease in CCA-IMT and CFA-IMT. This difference achieved significance after 8 weeks of treatment, but a trend was visible at 4 weeks. These rapid changes in IMT may be attributable to an anti-inflammatory effect. IMT measurement may be a useful tool to rapidly assess the effect of drug treatment on the atherosclerotic process.
Aged↗
Recent patterns and mechanisms of carbon exchange by terrestrial ecosystems.
Knowledge of carbon exchange between the atmosphere, land and the oceans is important, given that the terrestrial and marine environments are currently absorbing about half of the carbon dioxide that is emitted by fossil-fuel combustion. This carbon uptake is therefore limiting the extent of atmospheric and climatic change, but its long-term nature remains uncertain. Here we provide an overview of the current state of knowledge of global and regional patterns of carbon exchange by terrestrial ecosystems. Atmospheric carbon dioxide and oxygen data confirm that the terrestrial biosphere was largely neutral with respect to net carbon exchange during the 1980s, but became a net carbon sink in the 1990s. This recent sink can be largely attributed to northern extratropical areas, and is roughly split between North America and Eurasia. Tropical land areas, however, were approximately in balance with respect to carbon exchange, implying a carbon sink that offset emissions due to tropical deforestation. The evolution of the terrestrial carbon sink is largely the result of changes in land use over time, such as regrowth on abandoned agricultural land and fire prevention, in addition to responses to environmental changes, such as longer growing seasons, and fertilization by carbon dioxide and nitrogen. Nevertheless, there remain considerable uncertainties as to the magnitude of the sink in different regions and the contribution of different processes.
Journal Article↗
Molecular dynamics in the endgame of protein structure prediction.
In order adequately to sample conformational space, methods for protein structure prediction make necessary simplifications that also prevent them from being as accurate as desired. Thus, the idea of feeding them, hierarchically, into a more accurate method that samples less effectively was introduced a decade ago but has not met with more than limited success in a few isolated instances. Ideally, the final stages should be able to identify the native state, show a good correlation with native similarity in order to add value to the selection process, and refine the structures even further. In this work, we explore the possibility of using state-of-the-art explicit solvent molecular dynamics and implicit solvent free energy calculations to accomplish all three of those objectives on 12 small, single-domain proteins, four each of alpha, beta and mixed topologies. We find that this approach is very successful in ranking the native and also enhances the structure selection of predictions generated from the Rosetta method.
Automation↗
Protein structure prediction and structural genomics.
Genome sequencing projects are producing linear amino acid sequences, but full understanding of the biological role of these proteins will require knowledge of their structure and function. Although experimental structure determination methods are providing high-resolution structure information about a subset of the proteins, computational structure prediction methods will provide valuable information for the large fraction of sequences whose structures will not be determined experimentally. The first class of protein structure prediction methods, including threading and comparative modeling, rely on detectable similarity spanning most of the modeled sequence and at least one known structure. The second class of methods, de novo or ab initio methods, predict the structure from sequence alone, without relying on similarity at the fold level between the modeled sequence and any of the known structures. In this Viewpoint, we begin by describing the essential features of the methods, the accuracy of the models, and their application to the prediction and understanding of protein function, both for single proteins and on the scale of whole genomes. We then discuss the important role that protein structure prediction methods play in the growing worldwide effort in structural genomics.
Amino Acid Sequence↗
Experimental autoimmune uveoretinitis in mice (Biozzi ABH and NOD) expressing the autoimmune-associated H-2A(g7) molecule: identification of a uveitogenic epitope.
To determine whether Biozzi ABH (H-2A(g7)) mice were susceptible to chronic experimental autoimmune uveoretinitis (EAU). Biozzi ABH were immunized with the two retinal antigens, interphotoreceptor retinoid binding protein (IRBP) and soluble antigen (S-Ag). Biozzi ABH mice were found to be susceptible to EAU induction with native bovine IRBP. Recombinant protein domains were used to identify IRBP domain 2 (EcR2) as the uveitogenic domain. Histopathological examination indicated that EcR2-induced disease was of a chronic, non-destructive nature in the Biozzi ABH. Using synthetic overlapping peptides corresponding to EcR2, a uveitogenic and immunogenic epitope was identified corresponding to human IRBP511-530. Non-obese diabetic (NOD) mice share the same MHC class II (H-2A(g7)) molecule as the Biozzi ABH, and were also found to be susceptible to EAU induction with EcR2. This study has identified a novel mouse model of EAU, whereby disease is of a chronic, non-destructive nature, which has potential to be used in immune manipulation and neuroprotection studies.
Animals↗
Conversion of monomeric protein L to an obligate dimer by computational protein design.
Protein L consists of a single alpha-helix packed on a four-stranded beta-sheet formed by two symmetrically opposed beta-hairpins. We use a computer-based protein design procedure to stabilize a domain-swapped dimer of protein L in which the second beta-turn straightens and the C-terminal strand inserts into the beta-sheet of the partner. The designed obligate dimer contains three mutations (A52V, N53P, and G55A) and has a dissociation constant of approximately 700 pM, which is comparable to the dissociation constant of many naturally occurring protein dimers. The structure of the dimer has been determined by x-ray crystallography and is close to the in silico model.
Bacterial Proteins↗
Consistent land- and atmosphere-based U.S. carbon sink estimates.
For the period 1980-89, we estimate a carbon sink in the coterminous United States between 0.30 and 0.58 petagrams of carbon per year (petagrams of carbon = 10(15) grams of carbon). The net carbon flux from the atmosphere to the land was higher, 0.37 to 0.71 petagrams of carbon per year, because a net flux of 0.07 to 0.13 petagrams of carbon per year was exported by rivers and commerce and returned to the atmosphere elsewhere. These land-based estimates are larger than those from previous studies (0.08 to 0.35 petagrams of carbon per year) because of the inclusion of additional processes and revised estimates of some component fluxes. Although component estimates are uncertain, about one-half of the total is outside the forest sector. We also estimated the sink using atmospheric models and the atmospheric concentration of carbon dioxide (the tracer-transport inversion method). The range of results from the atmosphere-based inversions contains the land-based estimates. Atmosphere- and land-based estimates are thus consistent, within the large ranges of uncertainty for both methods. Atmosphere-based results for 1980-89 are similar to those for 1985-89 and 1990-94, indicating a relatively stable U.S. sink throughout the period.
Agriculture↗
Post-translational modification of the N-terminal His tag interferes with the crystallization of the wild-type and mutant SH3 domains from chicken src tyrosine kinase.
Structural studies of the wild type and mutants of the src SH3 domain were initiated to elucidate the correlation of the native-state topology with protein thermostability and folding kinetics. An extra mass of 178 Da arising from the post-translational modification at the N-terminal His tag was observed. The spontaneous alpha-N-6 gluconoylation at the amino group of the His-tagged SH3 domain contributed to the observed extra mass. The partial modification of the N-terminal His-tag produced heterogeneity, both in size and in charge, in the Escherichia coli expressed SH3 domain. The removal of the His tag from the SH3 domain was essential for the crystallization of both wild-type and mutant src SH3. Both the wild type and the W43I mutant were crystallized by hanging-drop vapor diffusion and are in the hexagonal space group P6(5)22 with one molecule in the asymmetric unit. Data sets were collected to 1.8 and 1.95 A resolution for the the wild type and the W43I mutant, respectively.
Amino Acid Sequence↗
Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation.
This study explores the use of multiple sequence alignment (MSA) information and global measures of hydrophobic core formation for improving the Rosetta ab initio protein structure prediction method. The most effective use of the MSA information is achieved by carrying out independent folding simulations for a subset of the homologous sequences in the MSA and then identifying the free energy minima common to all folded sequences via simultaneous clustering of the independent folding runs. Global measures of hydrophobic core formation, using ellipsoidal rather than spherical representations of the hydrophobic core, are found to be useful in removing non-native conformations before cluster analysis. Through this combination of MSA information and global measures of protein core formation, we significantly increase the performance of Rosetta on a challenging test set. Proteins 2001;43:1-11.
Algorithms↗
Evidence for linkage of familial Diamond-Blackfan anemia to chromosome 8p23.3-p22 and for non-19q non-8p disease.
Diamond-Blackfan anemia (DBA) is a rare congenital hypoplastic anemia that usually presents early in infancy and is inherited in 10% to 20% of cases. Linkage analysis has shown that DBA in many of both dominant and recessive DBA families mapped to chromosome 19q13.2 leading to the cloning of a gene on chromosome 19q13.2 that encodes a ribosomal protein, RPS19. However, subsequently, mutations of the RPS19 gene have only been identified in 25% of all patients with DBA. This study analyzed 14 multiplex DBA families, 9 of which had 19q13.2 haplotypes inconsistent with 19q linkage. A genome-wide search for linked loci suggested the presence of a second DBA locus in a 26.4-centimorgan (cM) interval on human chromosome 8p. Subsequently, 24 additional DBA families were ascertained and all 38 families were analyzed with additional polymorphic markers on chromosome 8p. In total, 18 of 38 families were consistent with linkage to chromosome 8p with a maximal LOD score with heterogeneity of 3.55 at D8S277 assuming 90% penetrance. The results indicate the existence of a second DBA gene in the 26.4-cM telomeric region of human chromosome 8p23.3-p22, most likely within an 8.1-cM interval flanked by D8S518 and D8S1825. Seven families were inconsistent with linkage to 8p or 19q and did not reveal mutations in the RPS19 gene, suggesting further genetic heterogeneity. (Blood. 2001;97:2145-2150)
Chromosomes, Human, Pair 19↗
Different therapeutic outcomes in experimental allergic encephalomyelitis dependent upon the mode of delivery of IL-10: a comparison of the effects of protein, adenoviral or retroviral IL-10 delivery into the central nervous system.
Experimental allergic encephalomyelitis (EAE) is a CNS autoimmune disease mediated by the action of CD4(+) T cells, macrophages, and proinflammatory cytokines. IL-10 is a cytokine shown to have many anti-inflammatory properties. Studies have shown both inhibition and exacerbation of EAE after systemic IL-10 protein administration. We have compared the inhibitory effect in EAE of Il10 gene delivery in the CNS. Fibroblasts transduced with retroviral vectors expressing IL-10 could inhibit EAE. This was not associated with a prevention of cellular recruitment but an alteration in their phenotype, notably an increase in the numbers of CD8(+) T and B cells. In marked contrast, CNS delivery of adenovirus coding for mouse IL-10 or IL-10 protein performed over a wide dose range failed to inhibit disease, despite producing similar or greater amounts of IL-10 protein. Thus the action of IL-10 may differ depending on the local cytokine microenvironment produced by the gene-secreting cell types.
Adenoviridae↗
Prospects for ab initio protein structural genomics.
We present the results of a large-scale testing of the ROSETTA method for ab initio protein structure prediction. Models were generated for two independently generated lists of small proteins (up to 150 amino acid residues), and the results were evaluated using traditional rmsd based measures and a novel measure based on the structure-based comparison of the models to the structures in the PDB using DALI. For 111 of 136 all alpha and alpha/beta proteins 50 to 150 residues in length, the method produced at least one model within 7 A rmsd of the native structure in 1000 attempts. For 60 of these proteins, the closest structure match in the PDB to at least one of the ten most frequently generated conformations was found to be structurally related (four standard deviations above background) to the native protein. These results suggest that ab initio structure prediction approaches may soon be useful for generating low resolution models and identifying distantly related proteins with similar structures and perhaps functions for these classes of proteins on the genome scale.
Computer Simulation↗
A randomized, controlled trial of remacemide for motor fluctuations in Parkinson's disease.
BACKGROUND: Preclinical studies suggest that glutamate antagonists help ameliorate motor fluctuations in patients with PD treated with levodopa. METHODS: In a multicenter, randomized, double-blind, placebo-controlled, parallel-group, dose-ranging study, the authors assessed the safety, tolerability, and efficacy of the glutamate receptor blocker remacemide hydrochloride in 279 patients with motor fluctuations treated with levodopa. The primary objective was to assess the short-term tolerability and safety of four dosage levels of remacemide during 7 weeks of treatment. Patients were also monitored with home diaries and the Unified PD Rating Scale (UPDRS) to collect preliminary data on treatment efficacy. RESULTS: Remacemide was well tolerated up to a dosage of 300 mg/d on a twice daily schedule and 600 mg/d on a four times daily schedule. The most common dosage-related adverse events were dizziness and nausea, as observed in previous studies of remacemide. The percent "on" time and motor UPDRS scores showed trends toward improvement in the patients treated with 150 and 300 mg/d remacemide compared with placebo-treated patients, although these improvements were not significant. CONCLUSION: Remacemide is a safe and tolerable adjunct to dopaminergic therapy for patients with PD and motor fluctuations. Although this study had limited power to detect therapeutic effects, the observed improvement is consistent with studies of non-human primates with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced parkinsonian signs and symptoms. Additional studies are warranted to confirm these results over an extended period of observation, and to explore the potential neuroprotective effects of remacemide in slowing the progression of PD.
Acetamides↗
Circularization changes the folding transition state of the src SH3 domain.
Native state topology has been implicated as a major determinant of protein-folding mechanisms. Here, we test experimentally the robustness of the src SH3-domain folding transition state to changes in topology by covalently constraining regions of the protein with disulfide crosslinks and then performing kinetic analysis on point mutations in the context of these modified proteins. Circularization (crosslinking the N and C termini) of the src SH3 domain makes the protein topologically symmetric and causes delocalization of structure in the transition state ensemble suggesting a change in the folding mechanism. In contrast, crosslinking a single structural element (the distal beta-hairpin) which is an essential part of the transition state, results in a protein that folds 30 times faster, but does not change the distribution of structure in the transition state. As the transition states of distantly related SH3 domains were previously found to be very similar, we conclude that the free energy landscape of this protein family contains deep features which are relatively insensitive to sequence variations but can be altered by changes in topology.
Amino Acid Substitution↗
2.1 and 1.8 A average C(alpha) RMSD structure predictions on two small proteins, HP-36 and s15.
On two different small proteins, the 36-mer villin headpiece domain (HP-36) and the 65-mer structured region of ribosomal protein (S15), several model predictions from the ab initio approach Rosetta were subjected to molecular dynamics simulations for refinement. After clustering the resulting trajectories into conformational families, the average molecular mechanics--Poisson Boltzmann/surface area (MM-PBSA) free energies and alpha carbon (C(alpha)) RMSDs were then calculated for each family. Those conformational families with the lowest average free energies also contained the best C(alpha) RMSD structures (1.4 A for S15 and HP-36 core) and the lowest average C(alpha) RMSDs (1.8 A for S15, 2.1 A for HP-36 core). For comparison, control simulations starting with the two experimental structures were very stable, each consisting of a single conformational family, with an average C(alpha) RMSD of 1.3 A for S15 and 1.2 A for HP-36 core (1.9 A over all residues). In addition, the average free energies' ranks (Spearman rank, r(s)) correlate well with the average C(alpha) RMSDs (r(s) = 0.77 for HP-36, r(s) = 0.83 for S15). Molecular dynamics simulations combined with the MM--PBSA free energy function provide a potentially powerful tool for the protein structure prediction community in allowing for both high-resolution structural refinement and accurate ranking of model predictions. With all of the information that genomics is now providing, this methodology may allow for advances in going from sequence to structure.
Models, Molecular↗
We need both computer models and experiments.
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Computer Simulation↗
The evolving practice of genetic counseling.
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Genetic Counseling↗