Footprint phenotypes: structural models of DNA-binding proteins from chemical modification analysis of DNA.
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Bacterial Proteins↗
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Results for “Models, Structural”
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LTP--a structural model to explain the inconsistencies.
One of the major controversies in neuroscience concerns whether the expression of long-term potentiation (LTP) is a pre- or postsynaptic phenomenon, with apparently contradictory data being the norm. The model that is outlined in this article combines anatomical and electrophysiological evidence to allow apparently contradictory data to be compatible. Development of LTP involves both influx of Ca2+ through NMDA receptors, and activation of another factor, perhaps the metabotropic glutamate receptor. These two processes might result, respectively, in the insertion of activation of additional postsynaptic receptors, and the growth of microfilaments that could split simple synapses into perforated synapses, consisting of multiple active zones. Whether the latter occurred, and at what rate, would be likely to depend on multiple factors, such as temperature, the metabolic state of the cell, buffering of Ca2+, and the concentration of factors such as nitric oxide. These subtle experimental variables would thus determine whether the dominant effect observed was pre- or postsynaptic.
Long-Term Potentiation↗
The relation of social support and working environment to medical variables associated with elevated blood pressure in young males: a structural model.
The object of the present study was to examine the interaction of working environment factors and the individual social support network with medical variables related to blood pressure elevations in young (mean age = 28 years) hypertensives. The results of path analyses reveal that the medical variables which explained a significant amount of the variation in systolic blood pressure were blood hemoglobin, plasma adrenaline and relative weight. High relative weight was associated with a low level of employment security and high plasma adrenaline with a poor self-reported social network as well as a job providing few possibilities for learning new things. High levels of diastolic pressure were associated with elevated hemoglobin levels, increased heart rate and low plasma renin activity. Increased heart rate was influenced by a lack of 'anger' coping in conflict situations at work and a low number of contacts with acquaintances. Working environment and social support are hypothesized to assert their influence through increased sympathetic stimulation mediated by limbic-hypothalamic discharge.
Adaptation, Psychological↗
Effects of early adolescent drug use on cognitive efficacy in early-late adolescence: a developmental structural model.
Despite an accumulated body of research evidence that documents the negative physical consequences of chronic alcohol and drug use, it is less clear whether the use of these same substances produces impaired cognitive abilities during the early stages of use. Early drug use may impede acquisition of critical thinking skills and hinder the learning of important cognitive strategies required for successful transition to adulthood. To better understand these relations, longitudinal latent-variable analyses were used to examine the effects of early adolescent drug use on early-late adolescent cognitive efficacy. Latent factors of polydrug use, behavioral control, and cognitive efficacy were hypothesized in early adolescence, the latter two controlling for potential spurious relations. At outcome, six constructs were hypothesized tapping polydrug use, cognitive mastery, self-reinforcement, problem-solving confidence, decision-making skills, and cognitive and affective self-management strategies. Models were psychometrically sound and accounted for large portions of variance. Early adolescent drug use had a small but significant negative effect on cognitive and affective self-management strategies. By the 12th grade, linkages between drug use and cognitive functioning were of larger magnitude than long-term influences, perhaps reinforcing the argument that deficits in cognitive skills are developmentally delayed and surface only with exacerbated or persistent drug use. Overall, specific effects of drug use adversely influenced important cognitive skills that may be critically related to functioning in both interpersonal and intrapersonal domains.
Adolescent↗
Track structure model for damage to mammalian cell cultures during solar proton events.
Solar proton events (SPEs) occur infrequently and unpredictably, thus representing a potential hazard to interplanetary space missions. Biological damage from SPEs will be produced principally through secondary electron production in tissue, including important contributions due to delta rays from nuclear reaction products. We review methods for estimating the biological effectiveness of SPEs using a high energy proton model and the parametric cellular track model. Results of the model are presented for several of the historically largest flares using typical levels and body shielding.
Animals↗
A structural model of menopausal depression in Korean women.
The purpose of this study was to develop and test a hypothetical model of predicting depression experienced by women during menopause. The subjects were menopausal women between 45 and 55 years of age, conveniently selected in two Korean cities. The instruments used in collecting data were scales for attitudes towards menopause and aging, scales for social support, scales for social conflicts, and the CES-D scale. Data were collected from 305 subjects through self-reported questionnaires. The data were analyzed using the LISREL program. The results of this study confirm that the important variables in the prediction of menopausal depression are educational and economic statuses, and perceived health status, and that the mediating variables are attitudes towards menopause and aging, social support, and social conflicts. Accordingly, the development of comprehensive intervention programs for decreasing menopausal depression should consider all of these variables.
Aging↗
Full-length cDNA cloning and protein three-dimensional structure modeling of porcine prothrombin.
Prothrombin is a vitamin K-dependent serine protease and plays pivotal roles in both procoagulant and anticoagulant pathway of hemostasis. In this study, we cloned the full-length cDNA of porcine prothrombin by cDNA library screening and SMART RACE technique. The full-length cDNA is 2027 bp, with a 1869 bp Open Reading Frame (ORF) coding 623 amino acids. The deduced protein of porcine prothrombin contains signal peptide, propeptide, Gla domain, two kringle domains and trypsin domain. Porcine prothrombin shares 86.15% nucleotide similarity and 83% amino acid similarity with human prothrombin. The trypsin domain is highly conserved between the two species with 92.1% amino acid identity. Macromolecular interaction sites comparison between porcine and human prothrombin suggests that the Gla domain in porcine prothrombin contains an additional potential gamma-carboxyglutamic acid site. However, a thrombin cleavage site (Arg284-Thr285) in its light chain is lost. When thrombin heavy chain is concerned, the most important functional sites such as catalytic triad DHS, RGD site, Na+ binding site and anion-binding exosite-I and II are highly conserved. However, great differences have been observed between residues 145 and 158 of heavy chain which is associated with thrombomodulin binding. Two important limited proteolysis sites at Ala150 and Lys154 were lost in porcine sequence, which would affect epsilon-thrombin and gammaT-thrombin generation. Comparison on 3-D protein models demonstrates that these proteins are obviously different in autolysis loop (Lys145 to Gly155). Compared with that of human prothrombin, variation at critical recognition sites would likely alter its binding affinity and reaction velocity, which would contribute to coagulation disorder when porcine liver is transplanted into human body.
1-Carboxyglutamic Acid↗
Cloning, functional identification and structural modelling of Vitis vinifera S-adenosylmethionine decarboxylase.
In this paper we report the cloning and full sequencing of S-adenosylmethionine decarboxylase (SAMDC, EC 4.1.1.50) cDNA from Vitis vinifera L. (VV) leaves, an enzyme belonging to the polyamine biosynthetic pathway, which appears to play an important role in the regulation of plant growth and development. The presence of two overlapping ORFs (tiny ORF and small ORF) upstream of the main ORF is reported in the Vitis cDNA. When the Vitis SAMDC cDNA was expressed in yeast without the two upstream ORFs, the resulting activity was about 50 times higher than the activity obtained with the full cDNA. These results demonstrated the strong regulatory activity of the tiny and small ORFs. RT-PCR expression analysis showed evidence of a similar mRNA level in all the tissues tested, with the exception of the petioles. The VV SAMDC was also modelled using its homologues from Solanum tuberosum and Homo sapiens as template. The present work confirmed, for the first time in a woody plant of worldwide economic interest such as grapevine, the presence of a regulatory mechanism of SAMDC, enzyme that has a well-established importance in the modulation of plant growth and development.
Adenosylmethionine Decarboxylase↗
Evolutionarily stable transition rates in a stage-structured model. An application to the analysis of size distributions of badges of social status.
This paper deals with the adaptive dynamics associated to a hierarchical non-linear discrete population model with a general transition matrix. In the model, individuals are categorized into n dominance classes, newborns lie in the subordinate class, and it is considered as evolutionary trait a vector eta of probabilities of transition among classes. For this trait, we obtain the evolutionary singular strategy and prove its neutral evolutionary stability. Finally, we obtain conditions for the invading potential of such a strategy, which is sufficient for the convergence stability of the latter. With the help of the previous results, we provide an explanation for the bimodal distribution of badges of status observed in the Siskin (Carduelis spinus). In the Siskin, as in several bird species, patches of pigmented plumage signal the dominance status of the bearer to opponents, and central to the discussion on the evolution of status signalling is the understanding of which should be the frequency distribution of badge sizes. Though some simple verbal models predicted a bimodal distribution, up to now most species display normal distributions and bimodality has only been described for the Siskin. In this paper, we give conditions leading to one of these two distributions in terms of the survival, fecundity and aggression rates in each dominance class.
Animals↗
Outcome of a workshop on archiving structural models of biological macromolecules.
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Genomics↗
An evaluation of a structural model for studies of the initiation of dieting among adolescent girls.
A model proposed to elucidate the sociopsychological processes involved in the initiation of dieting behavior among female adolescents was evaluated in the present study. The model incorporates social influence (as modeling, conformity, and compliance), autonomous functioning (as conformity disposition, individuation, self-reliance, and locus of control), skill-related functioning (as interpersonal negotiation skills and social self-efficacy), and parental style (in care and overprotection). It was investigated using path analytic procedures. One hundred forty-eight female high school students, aged between 13 and 16 years, completed a battery of questionnaires and were also interviewed individually. The results emphasized that adolescent dieting needs to be understood as a complex multicausal phenomenon. Adolescents' perceptions of direct pressure from their parents to diet was found to be a significant predictor of dieting, and perceived parental encouragement of autonomy, and self-confidence were associated with less dieting behavior. Moreover, whereas body mass index (BMI) and body dissatisfaction significantly predicted dieting, the three sociopsychological variables remained significant predictors of dieting when taking BMI into account, and perceived parent influence to diet remained a significant predictor when taking body dissatisfaction into account. The effect of autonomous functioning on dieting was mediated by body dissatisfaction. The findings suggest a reformulated model for use in large-scale longitudinal investigations.
Adolescent↗
Growth of mixed cultures on mixtures of substitutable substrates: the operating diagram for a structured model.
The growth of mixed microbial cultures on mixtures of substrates is a problem of fundamental biological interest. In the last two decades, several unstructured models of mixed-substrate growth have been studied. It is well known, however, that the growth patterns in mixed-substrate environments are dictated by the enzymes that catalyse the transport of substrates into the cell. We have shown previously that a model taking due account of transport enzymes captures and explains all the observed patterns of growth of a single species on two substitutable substrates (J. Theor. Biol. 190 (1998) 241). Here, we extend the model to study the steady states of growth of two species on two substitutable substrates. The model is analysed to determine the conditions for existence and stability of the various steady states. Simulations are performed to determine the flow rates and feed concentrations at which both species coexist. We show that if the interaction between the two species is purely competitive, then at any given flow rate, coexistence is possible only if the ratio of the two feed concentrations lies within a certain interval; excessive supply of either one of the two substrates leads to annihilation of one of the species. This result simplifies the construction of the operating diagram for purely competing species. This is because the two-dimensional surface that bounds the flow rates and feed concentrations at which both species coexist has a particularly simple geometry: It is completely determined by only two coordinates, the flow rate and the ratio of the two feed concentrations. We also study commensalistic interactions between the two species by assuming that one of the species excretes a product that can support the growth of the other species. We show that such interactions enhance the coexistence region.
Bacteria↗
ColE1 plasmid replication: a simple kinetic description from a structured model.
Time constant analysis illustrates how a complex model for ColE-1-type plasmid replication can be reduced to a simple, realistic description of the overall replication kinetics. The analysis leads to the identification of the key parameters governing plasmid replication and to the estimation of parameters that are difficult to determine experimentally. The overall kinetics of ColE1-type plasmid replication are zerothorder in production and first order in dilution. Experimental data confirm our predictions. Similar analysis of the postulated mechanism for the action of the Rom protein reveals that it has no significant effect on plasmid replication dynamics.
Cell Cycle↗
Vaccination strategies and backward bifurcation in an age-since-infection structured model.
We consider models for a disease with acute and chronic infective stages, and variable infectivity and recovery rates, within the context of a vaccination campaign. Models for SIRS and SIS disease cycles exhibit backward bifurcations under certain conditions, which complicate the criteria for success of the vaccination campaign by making it possible to have stable endemic states when R(0)<1. We also show the extent to which the forms of the infectivity and recovery functions affect the possibility of backward bifurcations. SIR and SI models examined do not exhibit this behavior.
Acquired Immunodeficiency Syndrome↗
Structured models for heterosexual disease transmission.
An SIS model for a heterosexually transmitted disease with core and non-core compartments and a generalized recovery function P(t) is analyzed. It exhibits R0 threshold behavior and leads to discussions of stability with respect to choice of P(t), and of the effects of allowing recruitment between core and non-core groups.
Female↗
Similar structural models of the transmembrane proteins of Ebola and avian sarcoma viruses.
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Amino Acid Sequence↗
Psychopathy in women: structural modeling and comorbidity.
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Adult↗
The Cu(II) acetate complex of the heteroscorpionate ligand (2-hydroxy-3-t-butyl-methylphenyl)bis(3,5-dimethylpyrazolyl)methane: a structural model for copper-substituted serralysin and astacin.
Reaction of Cu(II) acetate with the deprotonated ligand (2-hydroxy-3-t-butyl-methylphenyl)bis(3,5-dimethylpyrazolyl)methane (L1O(-)) in methanol produced the complexes [(L1O)Cu(OAc)], a=9.275(2), b=11.641(5), c=13.532(3) A, alpha=69.62(1) degrees, beta=89.49(2) degrees, gamma=87.12(1) degrees, P1. The Cu adopts a distorted five-coordinate geometry where the two pyrazole nitrogen ligands and a bidentate acetate occupy the pseudoequatorial plane with the phenoxy oxygen in an apical position. This complex has a number of features in common with galactose oxidase and the copper-substituted endopeptidases serralysin and astacin.
Crystallography, X-Ray↗