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Novel gain-of-function mutations of platelet glycoprotein IBalpha by valine mutagenesis in the Cys209-Cys248 disulfide loop. Functional analysis under statis and dynamic conditions.

Platelet-type von Willebrand disease is a bleeding disorder resulting from gain-of-function mutations of glycoprotein (GP) Ibalpha that increase its affinity for von Willebrand factor (vWf). The two known naturally occurring mutations, G233V and M239V, both enrich the valine content of an already valine-rich region within the Cys(209)-Cys(248) disulfide loop. We tested the effect of converting other non-valine residues in this region to valine. Of 10 mutants expressed in CHO cells as components of GP Ib-IX complexes, four displayed a gain-of-function phenotype (G233V, D235V, K237V, and M239V) based on (125)I-vWf binding and adhesion to immobilized vWf. The remainder displayed loss-of-function phenotypes. The gain-of-function mutants bound vWf spontaneously and had a heightened response to low concentrations of ristocetin or botrocetin, whereas the loss-of-function mutants bound vWf more poorly than wild-type GP Ibalpha. No distinct gain- or loss-of-function conformations were identified with conformation-sensitive antibodies. Compared with cells expressing wild-type GP Ibalpha, cells expressing the gain-of-function mutants rolled significantly more slowly over immobilized vWf under flow than wild-type cells and were able to adhere to vWf coated at lower densities. In aggregate, these data indicate that the region of GP Ibalpha bounded by Asn(226) and Ala(244) regulates the affinity for vWf.

Amino Acid Sequence↗

Studies on thymus function. 3. Duration of thymic function.

The immune functions of neonatally thymectomized C3Hf mice exposed only temporarily to thymus function show a progressive decay with time in the absence of the thymus. The immune responses studied at different ages in the range of 100-600 days were: first-set rejection of H-2-compatible and incompatible skin allografts, second-set rejection of skin allografts, capacity of spleen cells to produce graft-versus-host reactions in F(1) hybrids, resistance to infection with mouse hepatitis virus, and response of spleen cells to phytohemagglutinin in vitro. These long-term studies had the purpose of determining the duration of the restoration induced by thymus function when the mice were exposed only temporarily to it. Different models were used but the two basic ones were: (a) mice grafted intraperitoneally at 15 days of age with a syngeneic thymus that was removed surgically at 10, 20, or 30 days after grafting, and (b) mice grafted at 15 days of age with allogeneic strain A thymoma or C57BL thymus, these representing situations in which there is spontaneous rejection of the restoring graft. In all the experimental models used, the animals were restored when tested at 100 days of age, but progressively became immunologically incapacitated at 200-300 days of age. From the more controlled experiments in which the restoring thymus graft was removed surgically, the following conclusions can be drawn. (a) A short exposure to a thymus graft can produce restoration of immune functions in neonatally thymectomized mice, but this restoration is not self-sustaining in the absence of the thymus and declines progressively with age. The decline usually starts at 200-300 days of age. (b) This was especially clear in experiments in which the same animal was tested twice in its lifetime for capacity to produce graft-versus-host reactions; these animals were competent at 100 days and became incompetent at 400 days of age. (c) The shortest period of thymic exposure studied was 10 days; if vascularization of the graft is taken into account, 2-3 days of thymic function are sufficient to produce restoration. (d) The immune decay observed in the thymectomized animals exposed temporarily to thymus was more profound than the physiological decay of immunity observed in control animals of similar age. (e) Of all the tests studied, the response of spleen cells to phytohemagglutinin was to be preserved the longest in animals exposed only temporarily to thymic function. The present results were interpreted in accordance with our previous findings indicating that a population of postthymic cells can be developed by temporary exposure of neonatally thymectomized animals to thymic function, but that this population is not self-sustaining in the absence of thymus and progressively decays by physiological attrition.

Age Factors↗

Functional dose-volume histograms for functionally heterogeneous normal organs.

Functional dose-volume histograms are proposed as an extension of the conventional dose-volume histograms, for quantitative assessment of three-dimensional radiation dose coverage of functionally heterogeneous normal organs. Examples are given to illustrate possible applications of this approach to the treatment of a brain tumour or a lung tumour, in which cases the distribution of the normal organ function can be obtained from functional dose-volume modalities. It is shown that a significant difference exists between the functional dose-volume histograms and the conventional dose-volume histograms when the normal organ function is non-uniformly distributed within the organ. Utilization of functional dose-volume histograms as the input for the calculation of normal tissue complication probabilities is discussed for different normal tissue structures.

Humans↗

Chain functions and scoring functions in genetic networks.

One of the grand challenges of system biology is to reconstruct the network of regulatory control among genes and proteins. High throughput data, particularly from expression experiments, may gradually make this possible in the future. Here we address two key ingredients in any such 'reverse engineering' effort: The choice of a biologically relevant, yet restricted, set of potential regulation functions, and the appropriate score to evaluate candidate regulatory relations. We propose a set of regulation functions which we call chain functions, and argue for their ubiquity in biological networks. We analyze their complexity and show that their number is exponentially smaller than all boolean functions of the same dimension. We define two new scores: one evaluating the fitness of a candidate set of regulators of a particular gene, and the other evaluating a candidate function. Both scores use established statistical methods. Finally, we test our methods on experimental gene expression data from the yeast galactose pathway. We show the utility of using chain functions and the improved inference using our scores in comparison to several extant scores. We demonstrate that the combined use of the two scores gives an extra advantage. We expect both chain functions and the new scores to be helpful in future attempts to infer regulatory networks.

Galactose↗

Basal ganglia functional connectivity based on a meta-analysis of 126 positron emission tomography and functional magnetic resonance imaging publications.

The striatum receives projections from the entire cerebral cortex. Different, but not mutually exclusive, models of corticostriatal connectivity have been proposed, including connectivity based on proximity, parallel loops, and a model of a tripartite division of the striatum into motor, associative, and limbic areas. All these models were largely based on studies of anatomic connectivity in nonhuman mammals and lesion studies in animals and humans. Functional neuroimaging has the potential to discern patterns of functional connectivity in humans in vivo. We analyzed the functional connectivity between the cortex and the striatum in a meta-analysis of 126 published functional neuroimaging studies. We mapped the peak activations listed in each publication into stereotaxic space and used standard functional imaging statistical methods to determine which cortical areas were most likely to coactivate with different parts of the striatum. The patterns of functional connectivity between the cortex and the different striatal nuclei are broadly consistent with the predictions of the parallel loop model. The rostrocaudal and dorsoventral patterns of corticostriatal functional connectivity are consistent with the tripartite division of the striatum into motor, associative, and limbic zones.

Basal Ganglia↗

Cloning and molecular characterization of a metabolic gene with development functions in Drosophila. I. Analysis of the head function of Punch.

In an effort to understand the functions of pterins throughout development we have been studying Punch (Pu), the structural gene for the enzyme GTP cyclohydrolase in Drosophila melanogaster. This enzyme catalyzes the first step in the pterin biosynthetic pathway. The Pu gene product is required for vital functions at two distinct stages in embryogenesis, and a pigmentation function in the eye of the young adult. We have localized the Pu region to 29 kb of DNA through the analysis of lesions present in Pu mutants. Since all of the mutations that were mapped affect the eye pigmentation function of Pu, and since this function is the best defined biochemically, we have concentrated on identifying and characterizing Pu products required for eye pigmentation in our initial examination of the cloned region. Four different transcripts from this region are expressed in the adult head. We show that one of these transcripts, the 1.7-kb species, is responsible for the pigmentation function through the analysis of mutant transcripts and the use of an in vitro translation assay. A 2-kb region lying within the locus is specifically required for this eye pigmentation function.

Animals↗

Functional divergence in the caspase gene family and altered functional constraints: statistical analysis and prediction.

In this article, we explore the pattern of type I functional divergence (i.e., altered functional constraints or site-specific rate difference) in the caspase gene family that is important for apoptosis (programmed cell death) and cytokine maturation. By taking advantage of substantial experimental data from caspases, the functional/structural basis of our posterior predictions from sequence analysis was extensively studied. Our results are as follows: (1) Phylogenetic analysis shows that the evolution of major caspase-mediated pathways has been facilitated by gene duplications, (2) type I functional divergence (altered functional constraints) is statistically significant between two major subfamilies, CED-3 and ICE, (3) 4 of 21 predicted amino acid residues (for site-specific rate difference between CED-3 and ICE) have been verified by experimental evidence, and (4) we found that some CED-3 caspases may inherit more ancestral functions, whereas other members may employ some recently derived functions. Our approach can be cost effective in functional genomics to make statistically sound predictions from amino acid sequences.

Amino Acid Sequence↗

Measuring higher level physical function in well-functioning older adults: expanding familiar approaches in the Health ABC study.

BACKGROUND: To evaluate development and progression of functional limitation and retain comparability with established approaches, we raised the measurement ceiling of commonly used self-report and performance-based measures of function. This study evaluated the utility and concurrent validity of these expanded measures. METHODS: The study population consisted of 3075 black and white men and women aged 70 to 79 years, with no reported mobility limitations or disability, participating in the Health, Aging, and Body Composition, or Health ABC study. Self-report measures were expanded by ascertaining ease of performance and including more demanding levels of some tasks. A single foot stand and narrow walk supplemented an established performance battery. For walking endurance, we developed the Long Distance Corridor Walk (LDCW), which includes distance covered in 2 minutes and the time to walk 400 m. RESULTS: The expanded self-report items identified one half of the men and one third of the women as exceptionally well functioning and 10% to 13% of men and 21% to 36% of women with lower capacity. The supplemented and rescored performance battery discriminated function over the full range. The LDCW further differentiated walking capacity at the high end and also identified a subgroup with limitations. The self-report and performance measures were significantly, but weakly, correlated (0.13-0.35) and were independent predictors of walking endurance. CONCLUSIONS: Well-functioning persons in their 70s exhibit a broad range of functional capacity readily ascertained by expanded self-report and performance tests. Significant associations among these measures support their concurrent validity, but generally weak correlations indicate they tap different, but important, dimensions of physical function.

Aged↗

Measuring disability and function in older women: psychometric properties of the late-life function and disability instrument.

BACKGROUND: The recent development of the Late-Life Function and Disability Instrument (LL-FDI) was an important contribution to the measurement of function and disability in older adults. The present study examined the psychometric properties and construct validity of the LL-FDI measure in a sample of older women. METHODS: Older black (n = 81) and white (n = 168) women completed the LL-FDI, several measures of physical function, and physical activity measures, and had their body mass index assessed at baseline of an ongoing prospective study. Confirmatory factor analyses (CFA) and correlational analyses were used to examine factorial and construct validity of the measure. RESULTS: The CFA, using an iterative model modification technique, resulted in an acceptable 15-item solution for the function component and an 8-item solution for the disability component. This abbreviated instrument demonstrated high correlations with the original scales. Construct validity for the LL-FDI was supported. Participants who demonstrated better physical function, reported being more active, and had lower body mass index reported less disability and less difficulty with function on the LL-FDI. CONCLUSIONS: The LL-FDI appears to be an effective instrument for assessing function and disability in older women, and the abbreviated version reported here may prove useful in certain circumstances due to its brevity. However, continued determination of the construct validity of the complete and abbreviated scales is recommended.

Aged↗

The impact of structural and functional characteristics of social relations as determinants of functional decline.

OBJECTIVES: This study examines whether aspects of social relations at baseline are related to functional decline at 5-year follow-up among nondisabled old men and women. METHODS: The investigation is based on baseline and follow-up data on 651 nondisabled 75-year-old persons in Jyväskylä (Finland) and Glostrup (Denmark). The analyses are performed separately for men and women. Possible selection problems were considered by using three outcome measures: first, functional decline among the survivors (n = 425); second, functional decline, including death, assuming that death is part of a general decline pattern (n = 565); and third, mortality (n = 651). Social relations were measured at baseline by several items focusing on the structure and function of the social network. RESULTS: In men, no weekly telephone contact was related to functional decline and mortality. Among women, less than weekly telephone contact, no membership in a retirement club, and not sewing for others were significantly related to functional decline and mortality. The associations were stronger when the dead were included in the outcome measure. DISCUSSION: The results point to the importance of social relations in the prevention of functional decline in older adults.

Activities of Daily Living↗

Rodent Y chromosome TSPY gene is functional in rat and non-functional in mouse.

Recombination is believed to prevent genetic deterioration in sexual populations because it allows conservation of functional genotypes by removing deleterious mutations. Moreover, evidence that non-recombining segments of a genome deteriorate is provided by genetic experiments in Drosophila and yeast. Y chromosomes generally do not recombine along most of their length, and thus Y chromosome genes, despite having been selectively maintained for their function, could be lost from the genome. Here we present definitive evidence that functional Y genes can be lost from the mammalian genome. TSPY genes must have been selectively maintained on the mammalian Y chromosome since before the radiation of eutheria, 80 million years ago, as they are found conserved on the Y chromosome in two mammalian orders: primate and artiodactyl. We have now identified TSPY on the rodent Y chromosome, in mouse and rat. The gene structure and expression of rat TSPY suggest that it is a functional, testis-specific gene, but the closely related mouse gene, Tspy, has clearly become non-functional, producing only low levels of aberrantly spliced transcripts. Thus TSPY lost its function in the mouse lineage after its divergence from the rat lineage. So, in the case of Tspy at least, the absence of recombination does appear to have led to the loss of a functional gene.

Animals↗

Changes in hand function in the aging adult as determined by the Jebsen Test of Hand Function.

The Jebsen Test of Hand Function is used to assess a broad range of hand functions required for activities of daily living. The time needed to complete a variety of subtests is measured, with high scores indicative of abnormality. Normative values have been established for men and women in two age groups: 20 to 59 years and 60 to 94 years. The purpose of this study was to determine whether hand function, as measured by the Jebsen test, declines with age in subjects over the age of 60 years. A total of 121 men and women were given the test and grouped into the following age categories: (1) 60 to 69 years, (2) 70 to 79 years, and (3) 80 to 89 years. Hand function decreased with age in both men and women. There were significant positive correlations between age and time needed to complete the various subtests, and analyses of variance revealed significant differences between subjects in their 80s and those in their 60s and 70s. In only a few tasks were there significant differences between men and women within any age group. Because of the decrease in normal function with age, measurements obtained with the Jebsen test in the elderly should be compared with normative values that are obtained from similarly aged subjects. [Hackel ME, Wolfe GA, Bang SM, Canfield JS. Changes in hand function in the aging adult as determined by the Jebsen Test of Hand Function.

Aged↗

The effect of graft function on FK506 plasma levels, dosages, and renal function, with particular reference to the liver.

Plasma FK506 was studied in 49 liver, 13 heart, 3 double-lung or heart-lung, and 21 kidney recipients. The levels were correlated with the drug doses used, kidney function, and liver function. In all varieties of recipients, there was an early rise in the FK506 plasma levels that occurred at the time of intravenous administration of the drug. At the same time or shortly after, there were increases in serum creatinine that were transitory except in liver recipients with continuing suboptimal graft function. The quality of hepatic function dominated all aspects of FK506 management in the liver recipients. Those who received well-functioning grafts could be given about the same drug doses as recipients of kidneys and the thoracic organs. Liver recipients with defective grafts had astronomical rises in plasma FK506, a high incidence of renal failure, and probably increased neurotoxicity. In kidney transplant recipients, the FK506 plasma levels and doses were essentially the same in patients with prompt versus delayed renal function. These studies have highlighted the necessity, first, of close pharmacologic monitoring of patients who are given FK506 in the presence of abnormal liver function, and second, of using smaller intravenous induction doses than in past practice.

Adolescent↗

Immunosenescence and macrophage functional plasticity: dysregulation of macrophage function by age-associated microenvironmental changes.

The macrophage lineage displays extreme functional and phenotypic heterogeneity, which appears to be because, in large part, of the ability of macrophages to functionally adapt to changes in their tissue microenvironment. This functional plasticity of macrophages plays a critical role in their ability to respond to tissue damage and/or infection and to contribute to clearance of damaged tissue and invading microorganisms, to recruitment of the adaptive immune system, and to resolution of the wound and of the immune response. Evidence has accumulated that environmental influences, such as stromal function and imbalances in hormones and cytokines, contribute significantly to the dysfunction of the adaptive immune system. The innate immune system also appears to be dysfunctional in aged animals and humans. In this review, the hypothesis is presented and discussed that the observed age-associated 'dysfunction' of macrophages is the result of their functional adaptation to the age-associated changes in tissue environments. The resultant loss of orchestration of the manifold functional capabilities of macrophages would undermine the efficacy of both the innate and adaptive immune systems. The macrophages appear to maintain functional plasticity during this dysregulation, making them a prime target of cytokine therapy that could enhance both innate and adaptive immune systems.

Aging↗

Autonomic and peripheral nerve function in early diabetic neuropathy. Possible influence of a novel aldose reductase inhibitor on autonomic function.

Autonomic and peripheral nerve functions as well as the possible short-term effect of a novel aldose reductase inhibitor (ARI) on neuropathy were evaluated in 30 male type I diabetics (age 25-44 years, mean 34; duration of diabetes 10-20 years, mean 34) with neurographic signs of peripheral neuropathy (PN). Autonomic neuropathy (AN) was established by the heart rate reactions to deep breathing (E/I ratio = vagal function) and to tilt (acceleration index = sympathetic and vagal functions; the brake index = vagal function). Twenty-nine patients, 13 with AN, completed the study. Among neurographic variables, only sural nerve function tests correlated with autonomic functions. Patients with AN showed significantly lower mean sensory action potential amplitudes (SAPA) sural, indicating axonal losses, than patients without AN (3.58 +/- 0.79 microV v. 7.34 +/- 1.12 microV; p less than 0.01). PN as measured by neurography did not improve during ARI treatment. On the other hand, vagal function (brake indices) improved (p less than 0.05) during ARI in AN patients.

Adult↗

The rice SPINDLY gene functions as a negative regulator of gibberellin signaling by controlling the suppressive function of the DELLA protein, SLR1, and modulating brassinosteroid synthesis.

SPINDLY (SPY) encodes an O-linked N-acetylglucosamine transferase that is considered to be a negative regulator of gibberellin (GA) signaling through an unknown mechanism. To understand the function of SPY in GA signaling in rice, we isolated a rice SPINDLY homolog (OsSPY) and produced knockdown transgenic plants in which OsSPY expression was reduced by introducing its antisense or RNAi construct. In knockdown plants, the enhanced elongation of lower internodes was correlated with decreased levels of OsSPY expression, similar to the spindly phenotype of Arabidopsis spy mutants, suggesting that OsSPY also functions as a negative factor in GA signaling in rice. The suppressive function of OsSPY in GA signaling was supported by the findings that the dwarfism was partially rescued and OsGA20ox2 (GA20 oxidase) expression was reduced in GA-deficient and GA-insensitive mutants by the knockdown of OsSPY function. The suppression of OsSPY function in a GA-insensitive mutant, gid2, also caused an increase in the phosphorylation of a rice DELLA protein, SLR1, but did not change the amount of SLR1. This indicates that the function of OsSPY in GA signaling is not via changes in the amount or stability of SLR1, but probably involves control of the suppressive function of SLR1. In addition to the GA-related phenotypes, OsSPY antisense and RNAi plants showed increased lamina joint bending, which is a brassinosteroid-related phenotype, indicating that OsSPY may play roles both in GA signaling and in the brassinosteroid pathway.

Amino Acid Sequence↗

Using the canonical modelling approach to simplify the simulation of function in functional-structural plant models.

Functional-structural plant models that include detailed mechanistic representation of underlying physiological processes can be expensive to construct and the resulting models can also be extremely complicated. On the other hand, purely empirical models are not able to simulate plant adaptability and response to different conditions. In this paper, we present an intermediate approach to modelling plant function that can simulate plant response without requiring detailed knowledge of underlying physiology. Plant function is modelled using a 'canonical' modelling approach, which uses compartment models with flux functions of a standard mathematical form, while plant structure is modelled using L-systems. Two modelling examples are used to demonstrate that canonical modelling can be used in conjunction with L-systems to create functional-structural plant models where function is represented either in an accurate and descriptive way, or in a more mechanistic and explanatory way. We conclude that canonical modelling provides a useful, flexible and relatively simple approach to modelling plant function at an intermediate level of abstraction.

Computer Simulation↗

Left ventricular function and oesophageal function in patients with angina pectoris and normal coronary angiograms.

Left ventricular function and oesophageal function (including oesophageal manometry and pH monitoring) were investigated and a psychiatric assessment carried out in 63 patients with angina pectoris and normal coronary angiograms. Twenty two (35%) patients had regional abnormalities of left ventricular wall motion (group A). Thirty six (57%) patients had an oesophageal abnormality (group B); 19 patients had gastro-oesophageal reflux and abnormal oesophageal motility, five had gastro-oesophageal reflux alone, and 12 had abnormal oesophageal motility alone. Only four had regional abnormalities of the left ventricular wall and abnormal oesophageal function. In nine (14%) patients left ventricular and oesophageal function were normal (group C). Psychiatric morbidity was significantly less common in group A than in groups B and C and was similar in group B and group C. A definite abnormality of left ventricular function, oesophageal function, or psychiatric morbidity is present in a high proportion of patients with angina pectoris and normal coronary angiograms and in some instances this may lead to specific treatment. If quantitative assessment of left ventricular function is normal, oesophageal investigations should be performed. Endoscopy of the upper gastrointestinal tract may demonstrate oesophageal disease, but, if findings are normal, oesophageal manometry and ambulatory oesophageal pH monitoring (including during treadmill exercise testing) should be carried out.

Adult↗