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The use of causal indicators in covariance structure models: some practical issues.

In conventional representations of covariance structure models, indicators are defined as linear functions of latent variables, plus error. In an alternative representation, constructs can be defined as linear functions of their indicators, called causal indicators, plus an error term. Such constructs are not latent variables but composite variables, and they have no indicators in the conventional sense. The presence of composite variables in a model can, in some situations, result in problems with identification of model parameters. Also, the use of causal indicators can produce models that imply zero correlation among many measured variables, a problem resolved only by the inclusion of a potentially large number of additional parameters. These phenomena are demonstrated with an example, and general principles underlying them are discussed. Remedies are described so as to allow for the evaluation of models that contain causal indicators.

Analysis of Variance↗

Sequences of three molluscan 5 S ribosomal RNAs confirm the validity of a dynamic secondary structure model.

The collection of known 5 S rRNA primary structures is enriched with the sequences from three mollusca, the snails Helix pomatia and Arion rufus, and the mussel Mytilus edulis. The three sequences can be fitted in a five-helix secondary structure model previously shown (De Wachter et al. (1982) Biochimie 64, 311-329) to apply to all 5 S RNAs regardless of their origin. One of the helices in this model can undergo a bulge-internal loop transition. Within the metazoan kingdom, the dimensions of each helix and loop are rigidly conserved, except for one helix which can comprise either 6 or 7 base pairs.

Animals↗

A physiological model for tert-amyl methyl ether and tert-amyl alcohol: hypothesis testing of model structures.

The oxygenate tert-amyl methyl ether (TAME) is a gasoline fuel additive used to reduce carbon monoxide in automobile emissions. To evaluate the relative health risk of TAME as a gasoline additive, information is needed on its pharmacokinetics and toxicity. The objective of this study was to use a physiologically-based pharmacokinetic (PBPK) model to describe the disposition of TAME and its major metabolite, tert-amyl alcohol (TAA), in male Fischer-344 rats. The model compartments for TAME and TAA were flow-limited. The TAME physiological model had 6 compartments: lung, liver, rapidly perfused tissues, slowly perfused tissues, fat, and kidney. The TAA model had 3 compartments: lung, liver, and total-body water. The 2 models were linked through metabolism of TAME to TAA in the liver. Model simulations were compared with data on blood concentrations of TAME and TAA taken from male Fischer-344 rats during and after a 6-hour inhalation exposure to 2500, 500, or 100 ppm TAME. The PBPK model predicted TAME pharmacokinetics when 2 saturable pathways for TAME oxidation were included. The TAA model, which included pathways for oxidation and glucuronide conjugation of TAA, underpredicted the experimental data collected at later times postexposure. To account for biological processes occurring during this time, three hypotheses were developed: nonspecific binding of TAA, diffusion-limited transport of TAA, and enterohepatic circulation of TAA glucuronide. These hypotheses were tested using three different model structures. Visual inspection and statistical evaluation involving maximum likelihood techniques indicated that the model incorporating nonspecific binding of TAA provided the best fit to the data. A correct model structure, based upon experimental data, statistical analyses, and biological interpretation, will allow a more accurate extrapolation to humans and, consequently, a greater understanding of human risk from exposure to TAME.

Administration, Inhalation↗

A tertiary structure model of the internal ribosome entry site (IRES) for methionine-independent initiation of translation.

Cricket paralysis-like viruses have a dicistronic positive-strand RNA genome. These viruses produce capsid proteins through internal ribosome entry site (IRES)-mediated translation. The IRES element of one of these viruses, Plautia stall intestine virus (PSIV), forms a pseudoknot immediately upstream from the capsid coding sequence, and initiates translation from other than methionine. Previously, we estimated that the IRES element of PSIV consists of seven stem-loops using the program MFOLD; however, experimental evidence of the predicted structures was not shown, except for stem-loop VI, which was responsible for formation of the pseudoknot. To determine the whole structure of the PSIV-IRES element, we introduced compensatory mutations into the upstream MFOLD-predicted helical segments. Mutation analysis showed that stem-loop V exists as predicted, but stem-loop IV is shorter than predicted. The structure of stem-loop III is different from predicted, and stem-loops I and II are not necessary for IRES activity. In addition, we identified two new pseudoknots in the IRES element of PSIV. The complementary sequence segments that are responsible for formation of the two pseudoknots are also observed in cricket paralysis virus (CrPV) and CrPV-like viruses such as Drosophila C virus (DCV), Rhopalosiphum padi virus (RhPV), himetobi P virus (HiPV), Triatoma virus (TrV), and black queen-cell virus (BQCV), although each sequence is distinct in each virus. Considering the three pseudoknots, we constructed a tertiary structure model of the PSIV-IRES element. This structural model is applicable to other CrPV-like viruses, indicating that other CrPV-like viruses can also initiate translation from other than methionine.

Base Pairing↗

A structural model of the orthorhombic Ga7Mn5 derived from its HREM image

The base-centered orthorhombic approximant Ga7Mn5 (a = 4.547(6) nm, b = 1.256(9) nm, c = 1.482(1) nm) consisting of flattened hexagon and concave octagon (called "crown" in this paper) subunits shown by high-resolution electron microscopy (HREM) was found to coexist with the Ga-Mn decagonal quasicrystal in the Ga58Mn42 alloy. The atomic sites in the flattened hexagon subunit have been deduced recently from a structural study of the orthorhombic Ga-Mn (1/1,1/1) approximant that consists only of the hexagon subunits. Similarly, the atomic sites in the crown subunit have been deduced from another orthorhombic Ga-Mn (2/1,1/1) approximant consisting only of the crown subunits. A structural model of the orthorhombic Ga7Mn5 can thus be constructed from these structural subunits. There are 332 Ga atoms and 232 Mn atoms in a unit cell, with a composition of Mn41.2Ga58.8, satisfying the symmetry of the space group Bmm2. The simulated electron diffraction patterns, [010] HREM images, and X-ray powder diffraction pattern based on this structural model agrees mainly with the experimental observations.

Journal Article↗

A simulation study of the effects of assignment of prior identity-by-descent probabilities to unselected sib pairs, in covariance-structure modeling of a quantitative-trait locus.

Sib pair-selection strategies, designed to identify the most informative sib pairs in order to detect a quantitative-trait locus (QTL), give rise to a missing-data problem in genetic covariance-structure modeling of QTL effects. After selection, phenotypic data are available for all sibs, but marker data-and, consequently, the identity-by-descent (IBD) probabilities-are available only in selected sib pairs. One possible solution to this missing-data problem is to assign prior IBD probabilities (i.e., expected values) to the unselected sib pairs. The effect of this assignment in genetic covariance-structure modeling is investigated in the present paper. Two maximum-likelihood approaches to estimation are considered, the pi-hat approach and the IBD-mixture approach. In the simulations, sample size, selection criteria, QTL-increaser allele frequency, and gene action are manipulated. The results indicate that the assignment of prior IBD probabilities results in serious estimation bias in the pi-hat approach. Bias is also present in the IBD-mixture approach, although here the bias is generally much smaller. The null distribution of the log-likelihood ratio (i.e., in absence of any QTL effect) does not follow the expected null distribution in the pi-hat approach after selection. In the IBD-mixture approach, the null distribution does agree with expectation.

Alleles↗

Advances in comparative protein-structure modelling.

Comparative modelling of protein 3D structure can now be applied with reasonable accuracy to ten times more protein sequences than the number of experimentally determined protein structures. A protein sequence that has at least 40% identity to a known structure can be modelled automatically with an accuracy approaching that of a low resolution X-ray structure or a medium resolution NMR structure. Currently, the errors in comparative models include mistakes in the packing of sidechains, in the conformation and shifts of the core segments and loops, and, most importantly, in an incorrect alignment of the modelled sequence with related known structures. Nevertheless, the number of applications in which comparative modelling has been proven to be useful has grown rapidly.

Crystallography, X-Ray↗

Bio-structural model of the human eye.

As part of a bio-engineering approach to study myopia, a structural model of the eye is proposed. The model is based on structural laws as employed by civil engineers, and on mechanical properties of the sclera and vitreous previously analyzed by the authors. The described structural behavior relates many loose clinical observations and indicates that progressive myopia should be considered a mechanical problem due to an abnormal vitreous pressure rather than an optics problem. From this bio-engineering approach, vitrectomy is suggested as the appropriate solution.

Biomechanical Phenomena↗

Is the in situ accessibility of the 16S rRNA of Escherichia coli for Cy3-labeled oligonucleotide probes predicted by a three-dimensional structure model of the 30S ribosomal subunit?

Systematic studies on the hybridization of fluorescently labeled, rRNA-targeted oligonucleotides have shown strong variations in in situ accessibility. Reliable predictions of target site accessibility would contribute to more-rational design of probes for the identification of individual microbial cells in their natural environments. During the past 3 years, numerous studies of the higher-order structure of the ribosome have advanced our understanding of its spatial conformation. These studies range from the identification of rRNA-rRNA interactions based on covariation analyses to physical imaging of the ribosome for the identification of protein-rRNA interactions. Here we reevaluate our Escherichia coli 16S rRNA in situ accessibility data with regard to a tertiary-structure model of the small subunit of the ribosome. We localized target sequences of 176 oligonucleotides on a 3.0-A-resolution three-dimensional (3D) model of the 30S ribosomal subunit. Little correlation was found between probe hybridization efficiency and the proximity of the probe target region to the surface of the 30S ribosomal subunit model. We attribute this to the fact that fluorescence in situ hybridization is performed on fixed cells containing denatured ribosomes, whereas 3D models of the ribosome are based on its native conformation. The effects of different fixation and hybridization protocols on the fluorescence signals conferred by a set of 10 representative probes were tested. The presence or absence of the strongly denaturing detergent sodium dodecyl sulfate had a much more pronounced effect than a change of fixative from paraformaldehyde to ethanol.

Escherichia coli↗

Evolution and physics in comparative protein structure modeling.

From a physical perspective, the native structure of a protein is a consequence of physical forces acting on the protein and solvent atoms during the folding process. From a biological perspective, the native structure of proteins is a result of evolution over millions of years. Correspondingly, there are two types of protein structure prediction methods, de novo prediction and comparative modeling. We review comparative protein structure modeling and discuss the incorporation of physical considerations into the modeling process. A good starting point for achieving this aim is provided by comparative modeling by satisfaction of spatial restraints. Incorporation of physical considerations is illustrated by an inclusion of solvation effects into the modeling of loops.

Biophysical Phenomena↗

Three-dimensional structural model analysis of the binding site of an inhibitor, nervonic acid, of both DNA polymerase beta and HIV-1 reverse transcriptase.

Previously, we reported the three-dimensional molecular interactions of nervonic acid (NA) with mammalian DNA polymerase beta (pol beta) [Mizushina et al. (1998) J. Biol. Chem. 274, 25599-25607]. By three-dimensional structural model analysis and comparison with the spatial positioning of specific amino acids binding to NA on pol beta (Leu11, Lys35, His51, and Thr79), we obtained supplementary information that allowed us to build a structural model of human immunodeficiency virus type-1 reverse transcriptase (HIV-1 RT). In HIV-1 RT, Leu100, Lys65, His235, and Thr386 corresponded to these four amino acid residues. These results suggested that the NA binding domains of pol beta and HIV-1 RT are three-dimensionally very similar. The effects of NA on HIV-1 RT are thought to be same as those on pol beta in binding to the rhombus of the four amino acid residues. NA dose-dependently inhibited the HIV-1 RT activity. For binding to pol beta, the kinetics were competitive when the rhombus was present on the DNA binding site. However, as the rhombus in HIV-1 RT was not present in the DNA binding site, the three-dimensional structure of the DNA binding site must be distorted, and subsequently the enzyme is inhibited non-competitively.

Amino Acid Sequence↗

Nucleotide sequence of Citrus limon 26S rRNA gene and secondary structure model of its RNA.

The complete nucleotide sequence of Citrus limon 26S rDNA has been determined. The sequence has been aligned with large ribosomal RNA (L-rRNA) sequences of Escherichia coli, Saccharomyces cerevisiae and Oryza sativa. Nine extensive expansion segments in dicot 26S rRNA relative to E. coli 23S rRNA have been identified and compared with analogous segments of monocot, yeast, amphibian and human L-rRNAs. A secondary structure model for lemon 26S rRNA has been derived based on the refined model of E. coli 23S rRNA. It has been compared with other eukaryotic L-rRNAs models in terms of location of functionally important regions. Origin and evolution of L-rRNA expansion segments are discussed.

Base Sequence↗

Measurement error in dietary assessment: an investigation using covariance structure models. Part II.

In Part I we presented a covariance structure model for analysing measurement error in the assessment of nitrogen intake. In this paper we include data on urine nitrogen excretion which allows a critical assessment of the model proposed. Inclusion of urine nitrogen data produces more pessimistic estimates of the quality of dietary intake measurements and shows that previous assumptions about independence of measurement error were wrong. This underscores the need for well founded assumptions in the analysis of measurement error.

Bayes Theorem↗

The sequence of the 5.8 S ribosomal RNA of the crustacean Artemia salina. With a proposal for a general secondary structure model for 5.8 S ribosomal RNA.

We report the primary structure of 5.8 S rRNA from the crustacean Artemia salina. The preparation shows length heterogeneity at the 5'-terminus, but consists of uninterrupted RNA chains, in contrast to some insect 5.8 S rRNAs, which consist of two chains of unequal length separated in the gene by a short spacer. The sequence was aligned with those of 11 other 5.8 S rRNAs and a general secondary structure model derived. It has four helical regions in common with the model of Nazar et al. (J. Biol. Chem. 250, 8591-8597 (1975)), but for a fifth helix a different base pairing scheme was found preferable, and the terminal sequences are presumed to bind to 28 S rRNA instead of binding to each other. In the case of yeast, where both the 5.8 S and 26 S rRNA sequences are known, the existence of five helices in 5.8 S rRNA is shown to be compatible with a 5.8 S - 26 S rRNA interaction model.

Animals↗

MODBASE, a database of annotated comparative protein structure models.

MODBASE is a queryable database of annotated comparative protein structure models. The models are derived by MODPIPE, an automated modeling pipeline relying on the programs PSI-BLAST and MODELLER. The database currently contains 3D models for substantial portions of approximately 17 000 proteins from 10 complete genomes, including those of Caenorhabditis elegans, Saccharomyces cerevisiae and Escherichia coli, as well as all the available sequences from Arabidopsis thaliana and Homo sapiens. The database also includes fold assignments and alignments on which the models were based. In addition, special care is taken to assess the quality of the models. ModBase is accessible through a web interface at http://guitar.rockefeller.edu/modbase/

Amino Acid Sequence↗

Symptom Effects on Employment in a Structural Model of Mental Illness and Treatment: Analysis of Patients with Schizophrenia.

BACKGROUND: There is a long tradition in the health and mental health economics literatures of estimating the impacts of disorders on employment and earnings. Several analyses have associated mental illness with poorer labor market outcomes, often using indicators of disorders to measure mental illness, but it is unclear to what extent unobserved medical treatment biases the estimated impacts of disorders on labor market outcomes. In this study we argue that in order to judge the true employment costs of mental illness and the potential benefits of treatment it is necessary to account for the structural relationship between treatment, symptoms, and employment outcomes. AIMS OF THE STUDY: The study proposes a structural model for understanding mental illness impacts on employment and empirically estimates one element of this structural model that links symptoms of schizophrenia to patients' employment status. In addition, we use our empirical estimates to simulate employment consequences of more effective treatment and reductions in symptom levels. EMPIRICAL METHODS: Our empirical analyses use a sample of 1,643 adults with a schizophrenia diagnosis. We predict the likelihood of three outcomes - not employed, employed in a sheltered or supported job, and employed in a non-supported job. Analyses include measures of demographic characteristics, illness history, location differences, and detailed symptom measures. RESULTS: We find that negative symptoms have a substantial adverse impact on participation in both non-supported jobs and in sheltered or supported jobs. The impacts on employment of other symptoms of schizophrenia are not as large, but significant effects are also found for symptoms of depression. Simulations suggest, however, that only one-third of consumers would be employed in any type of job even given a large reduction in symptom levels. DISCUSSION: Negative symptoms are particularly important for role functioning and employment. The marginal effect on employment of a reduction in negative symptoms is several times greater than the effect of a comparable reduction in positive symptoms. Moreover, the effect of an improvement in symptoms on employment is stronger for non-supported employment than for working in sheltered or supported employment. Although commonly measured symptoms of schizophrenia impact employment, greater control of symptoms alone is unlikely to lead to large increases in employment for persons with schizophrenia in the near term. IMPLICATIONS FOR HEALTH CARE PROVISION AND USE: These findings suggest that improved treatment that results in reduced symptom levels will increase rates of employment among persons with schizophrenia, but that large employment impacts probably also require more effective rehabilitative therapies that target improvement in functioning. IMPLICATION FOR POLICY: Expansions of supported employment opportunities and removal of work disincentives in public income-support programs are two additional measures that may help to increase employment participation.

Journal Article↗

Characterization of a structural model of membrane bound cytochrome c-550 from Bacillus subtilis.

A structural model of Bacillus subtilis cytochrome c-550 has been built based upon hydropathy analysis, sequence alignment, homology modeling, and energy minimization. The model has a single transmembrane alpha-helix and a water-soluble domain folded around covalently attached heme C. Physical measurements on purified, recombinant cytochrome c-550 have been made to test aspects of the model. Excitation at either 280 or 295 nm yields fluorescence with an emission maximum at 334 nm and a quantum yield of 25% relative to n-acetyltryptophanamide. The model places one (i.e., W115) of the two tryptophans of cytochrome c-550 in the heme domain and the second (i.e., W3) in the transmembrane domain. The indole ring of W115 is within 5 A of the heme macrocycle and is expected to be highly quenched via resonance energy transfer to the heme. In contrast, W3 is at the start of the putative transmembrane helix and could be located a considerable distance from the heme. Förster theory assigns a distance of 42 A from W3 to the heme. This distance is important in adjusting the relative positions of the membrane-spanning and heme-binding domains. Circular dichroism measurements in the ultraviolet region indicate increased alpha-helical content of B. subtilis cytochrome c compared to mitochondrial cytochrome c in support of an alpha-helical transmembrane domain. The ionic strength dependence of redox kinetics for cytochrome c-550 indicates an overall negative charge that is consistent with a calculated pI of 5.4. However, the charge distribution specified by the model indicates a surface for electron exchange that is different from the classical front face used by mitochondrial cytochrome c.

Amino Acid Sequence↗

Structural model of human ceruloplasmin based on internal triplication, hydrophilic/hydrophobic character, and secondary structure of domains.

A molecular model for the structure of human ceruloplasmin is proposed that is based on the determination of the complete amino acid sequence, studies of the products of limited proteolytic cleavage, calculations of the hydrophilic/hydrophobic character (hydropathy profile), and predictions of the local secondary structure. This multicopper oxidase (Mr approximately 132,000) consists of a single polypeptide chain (1046 amino acid residues) with four attached glucosamine oligosaccharides. Computer-assisted statistical analysis of the internal repetition in the amino acid sequence confirms that the entire polypeptide chain is divided into three contiguous homology units, each containing about 350 amino acid residues. Each homology unit is subdivided into three domains, designated A1, A2, and B, that differ in structure and probably in function. Calculations of the hydropathy profile and predictions of the secondary structure support a molecular model based on internal repetition of three homology units and help to identify characteristic features of the interdomain junctions. The alignment scores for internal duplication of pairings of the three homology units of ceruloplasmin exceed the scores yet reported for contiguous internal duplication of any other protein. This highly significant evidence for intragenic repetition suggests that the ceruloplasmin molecule evolved by tandem triplication of ancestral genes coding for a primordial copper oxidase.

Amino Acid Sequence↗