Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span

Background  

The statistical modeling of biomedical corpora could yield integrated, coarse-to-fine views of biological phenomena that complement discoveries made from analysis of molecular sequence and profiling data. Here, the potential of such modeling is demonstrated by examining the 5,225 free-text items in the Caenorhabditis Genetic Center (CGC) Bibliography using techniques from statistical information retrieval. Items in the CGC biomedical text corpus were modeled using the Latent Dirichlet Allocation (LDA) model. LDA is a hierarchical Bayesian model which represents a document as a random mixture over latent topics; each topic is characterized by a distribution over words.     

The shape of human gene family phylogenies

Background  

The shape of phylogenetic trees has been used to make inferences about the evolutionary process by comparing the shapes of actual phylogenies with those expected under simple models of the speciation process. Previous studies have focused on speciation events, but gene duplication is another lineage splitting event, analogous to speciation, and gene loss or deletion is analogous to extinction. Measures of the shape of gene family phylogenies can thus be used to investigate the processes of gene duplication and loss. We make the first systematic attempt to use tree shape to study gene duplication using human gene phylogenies.     

Enhanced recruitment of Th2 and CLA-negative lymphocytes by the S128R polymorphism of E-selectin

E-selectin is a cytokine-inducible endothelial cell adhesion molecule that binds a restricted population of T lymphocytes consisting of Th1 memory cells bearing the cutaneous lymphocyte Ag (CLA). A serine to arginine (S128R) polymorphism in E-selectin has been reported at increased frequency in patients with systemic lupus erythematosus and atherosclerosis. Here we tested the hypothesis that the S128R substitution may contribute to increased vascular disease by altering the number and/or phenotype of lymphocytes interacting with E-selectin under shear flow. We observed that CHO cell monolayers transfected with S128R recruited significantly greater numbers of unfractionated lymphocytes than monolayers expressing an equivalent density of wild-type (WT) E-selectin. Depletion of the CLA(+) subpopulation or generation of CLA(-) lymphoblasts abolished rolling and arrest on WT E-selectin, but left a residual population that interacted with S128R. Generation of Th subsets revealed preferential interaction of Th0 and Th2, but not Th1, cells with S128R compared with WT. However, only T cells of a memory phenotype interacted with S128R, since neither monolayer supported rolling of CD45RA(+) cells. Our results demonstrate that the S128R polymorphism extends the range of lymphocytes recruited by E-selectin, which may provide a mechanistic link between this polymorphism and vascular inflammatory disease.     

Modulation of the enkephalinergic phenotype of rat sympathetic neurons by hormonal and transynaptic mechanisms

Most sympathetic neurons contain one or more neuropeptides in addition to catecholamines. Although the regulation of catecholamines has been studied extensively, comparatively little is known about the regulation of neuropeptides. Since glucocorticoids and preganglionic innervation regulate catecholaminergic properties in chromaffin cells, we examined the effects of these factors on a co-localized neuropeptide, leucine enkephalin (L-Enk), in adult rat sympathetic neurons in vivo. Lowered serum glucocorticoid levels as a consequence of bilateral adrenalectomy resulted in a reduction of ganglionic L-Enk content that was reversed by exposure of adrenalectomized animals to the synthetic glucocorticoid, dexamethasone. Surgical denervation of the SCG eliminated L-Enk-IR preganglionic fibers and caused a dramatic increase in the number of L-Enk-IR neurons. Inhibition of the enkephalinergic component of the preganglionic innervation by chronic exposure to the opiate receptor antagonist naloxone increases the number of L-Enk-IR cell bodies and total ganglionic L-Enk content. None of the experimental manipulations noticeably altered the number or distribution of NPY-IR neurons, suggesting that the effects of glucocorticoids and the innervation on ganglionic L-Enk levels were specific and not simply an alteration of the biosynthetic state of the cells. These results demonstrate that circulating glucocorticoids and the preganglionic innervation regulate L-Enk levels in sympathetic neurons. Since both glucocorticoid levels and preganglionic activity are known to be altered by stressful stimuli, acute regulation of sympathetic L-Enk levels may constitute an important component of the autonomic response to stress. © 1993 John Wiley & Sons, Inc.     

A DIRECT METHOD FOR DETERMINING DOPAMINE SYNTHESIS AND OUTPUT OF DOPAMINE METABOLITES FROM BRAIN IN AWAKE ANIMALS

Abstract— A direct method for measuring the rate of dopamine (DA) synthesis and the DA metabolites by the brain of awake monkeys ( Macaca arctoides ) is described. The method utilizes a coupling of a measure of cerebral blood flow with the mass spectrometrically determined difference in the concentrations of the metabolite under study in plasma obtained from arterial and internal jugular bulb blood. For homovanillic acid (HVA) a consistent and highly significant veno-arterial (V-A) difference of 2.2 ± 0.4 ng/ml of plasma ( P < 0.0005) was found. When this V-A difference was coupled with a measure of cerebral blood flow it was determined that, in the awake monkey, the average output of HVA by brain was 113.4 ± 19.1ng/100g brain min⁻¹. There were large individual variations, however, between animals (range = 38-194 ng/100g brain min⁻¹). In contrast to HVA, no consistent V-A difference for dihydroxyphenylacetic acid (DOPAC) was found; i.e. the concentrations of DOPAC in plasma obtained from arterial and internal jugular bulb venous blood were essentially identical. These data indicate that, in contrast to the rat, in this non-human primate HVA is the major metabolic product of brain DA. Since HVA is the major metabolite of DA, production of HVA under steady state conditions gives a measure of DA synthesis by whole brain; i.e. the rate of DA synthesis by whole brain in the awake monkey is 113.4 ± 19.1ng/100g brain min⁻¹. It is suggested that this technique may be of value in both basic and applied types of studies.     

Growth cones of cultured sympathetic neurons contain adrenergic vesicles

The growth cones of dissociated rat sympathetic neurons developing in culture were fixed with potassium permanganate to visualize vesicular stores of norepinephrine through the formation of granular precipitates. It was found that growth cones contain numerous small granular vesicles (SGV) 40-60 nm in diameter. The majority of the SGV was present in the varicosity of the growth cone but SGV also occurred in filopodia. The SGV appeared in clusters or scattered throughout the varicosity. Treatment of the cultured neurons, before fixation, with reserpine, which depletes catecholamine stores by blocking uptake into vesicles, resulted in the presence of small clear vesicles. In contrast, growth cones of nonadrenergic sensory neurons dissociated from dorsal root ganglia and fixed with permanganate lacked SGV and possessed small clear vesicles. These observations indicate that the growth cones of cultured sympathetic neurons contain norepinephrine, suggest that the norepinephrine is stored in synaptic vesicles, and raise the question whether this transmitter plays a role in early axon-target cell interactions during synapse formation.     

A computer program for testing average partial association in three-way contingency tables (PARCAT).

PARCAT is a computer program which implements alternative tests for average partial association in three-way contingency tables within the framework of the product multiple hypergeometric probability model. Primary attention is directed at the relationship between two of the variables, controlling for the effects of a covariable. This approach is essentially a multivariate extension of the Cochran/Mantel-Haenszel test to sets of (s x r) tables. A set of scores such as uniform, ridits, or probits can be assigned to categories which are ordinally scaled. In particular, if ridit scores with midranks assigned for ties are utilized, this procedure is equivalent to a partial Kruskal-Wallis test when one variable is ordinally scaled, and is equivalent to a partial Spearman rank correlation test when both variables are ordinally scaled.