Phosphoinositide kinases.

Phosphatidylinositol, a component of eukaryotic cell membranes, is unique among phospholipids in that its head group can be phosphorylated at multiple free hydroxyls. Several phosphorylated derivatives of phosphatidylinositol, collectively termed phosphoinositides, have been identified in eukaryotic cells from yeast to mammals. Phosphoinositides are involved in the regulation of diverse cellular processes, including proliferation, survival, cytoskeletal organization, vesicle trafficking, glucose transport, and platelet function. The enzymes that phosphorylate phosphatidylinositol and its derivatives are termed phosphoinositide kinases. Recent advances have challenged previous hypotheses about the substrate selectivity of different phosphoinositide kinase families. Here we re-examine the pathways of phosphoinositide synthesis and the enzymes involved.

The usefulness of diagnostic tests on pericardial fluid.

STUDY OBJECTIVES: To determine the physical, chemical, and cellular characteristics of pericardial fluid in various disease states and to assess their diagnostic accuracies. SETTING: A metropolitan university hospital. DESIGN: Consecutive case series. PATIENTS: One hundred seventy-five hospital patients, aged 1 month to 87 years, who had undergone pericardiocentesis (n = 165) or control subjects who had undergone open heart surgery (n = 10) between 1984 and 1996. MEASUREMENTS: The appearance of pericardial fluid and results of chemistry tests, cell counts, cytologic studies, Gram's stain, and microbial cultures were obtained by chart review. The etiology of each pericardial fluid sample was determined using prospective diagnostic criteria. RESULTS: Exudates differed from transudates by higher leukocyte counts and ratios of fluid to serum lactate dehydrogenase levels. Fluid glucose levels were significantly less in exudates. Sensitivity for detecting exudates was high for specific gravity > 1.015 (90%), fluid total protein > 3.0 g/dL (97%), fluid to serum protein ratio > 0.5 (96%), fluid lactate dehydrogenase ratio > 0.6 (94%), and fluid to serum glucose ratio < 1.0 (85%). None of these indicators were specific. Fluid total protein and specific gravity were moderately correlated (r = 0.56). Fluid cytologic study had a sensitivity of 92% and specificity of 100% for malignant effusion. No other test was diagnostic for a specific etiology. Among infection-associated effusions, culture-positive fluid had more neutrophils, higher lactate dehydrogenase levels, and lower ratios of fluid to serum glucose than culture-negative (parainfective) fluid. CONCLUSIONS: Evaluation of pericardial fluid might be limited to cell count, glucose, protein, and lactate dehydrogenase determinations plus bacterial culture and cytology. While not used routinely, other tests that may be highly specific for particular diseases should be ordered only to confirm a high clinical suspicion.

A terminal dynamics model of the heartbeat.

It is widely assumed that heartbeat dynamics are chaotic, although there has been no evidence confirming such an opinion, and some evidence to the contrary. Additionally, the deterministic assumptions of such dynamics cannot be demonstrated. An alternative model is presented based upon the notion of terminal dynamics, which can more faithfully represent key features of the heartbeat: namely, piecewise determinism, and singular points between beats, which allow for adaptability while maintaining stability.

Multiple sets of basal factors initiate transcription by RNA polymerase II.

The minimal requirements for transcription initiation from supercoiled templates were determined for the two major forms of TATA-binding factors found in cell extracts, the 300-kDa B-TFIID and the 1000-kDa D-TFIID complexes. As had been observed for the TATA-binding protein (TBP) subunit (Parvin and Sharp, 1993), transcription from the IgH promoter minimally requires TFIID activity plus TFIIB and RNA polymerase II. This minimal reaction is only active on negatively supercoiled template DNA. In contrast, the supercoiled templates encoding the adenovirus major late promoter (MLP), or several other promoters, require the addition of TFIIF to the minimal reaction. Further addition of TFIIE and TFIIH boosts the level of transcription from these latter promoters but is not required. In contrast to the complete reaction on linear template, transcription from supercoiled IgH or MLP templates does not require the hydrolysis of the beta-gamma bond of ATP. Fourteen different core promoters were compared in complete and minimal basal transcription reactions reconstituted with one of the three TATA activities: TBP, B-TFIID, and D-TFIID. Of these 14 promoters, only the IgH was active in the absence of TFIIF, and the other promoters demonstrated different levels of transcription depending on which basal factors were present in reaction. It is proposed that a significant level of basal transcription only requires a minimal set of factors, and stimulation by upstream activators may in part be mediated by the inclusion of additional basal factors into the initiation reaction.

TATA-binding protein and associated factors in polymerase II and polymerase III transcription.

Transcription by RNA polymerase I (pol I), pol II, and pol III requires the TATA-binding protein (TBP). This protein functions in association with distinct TBP-associated factors (TAFs) which may specify the nature of the polymerase selected for initiation at a promoter site. In the pol III transcription system, the TBP-TAF complex is a component of the TFIIIB factor. This factor has been resolved into a TBP-TAF complex and another component, both of which are required for reconstitution of transcription by pol III. Neither the TBP-TAF complexes B-TFIID and D-TFIID, which were previously characterized as active for pol II transcription, nor TBP alone can complement pol III transcription reactions that are dependent upon the TBP-TAF subcomponent of TFIIIB. Surprisingly, the TBP-TAF subcomponent of TFIIIB is active in reconstitution of pol II transcription.

Composition of transcription factor B-TFIID.

Initiation of transcription by RNA polymerase II requires a TFIID factor, which can recognize the TATA element common to many promoters. Two distinct multisubunit TFIID factors can be resolved from extracts of mammalian cells, and both of them contain the well-characterized TATA-binding protein (TBP) and are capable of supporting RNA polymerase II transcription in an in vitro reaction system. The smaller complex, B-TFIID, was purified and its subunit composition was determined. B-TFIID consists of two subunits: the TBP and a TBP-associated factor (TAF) of 170 kDa. This TAF is specific for B-TFIID and appears not to be present in the D-TFIID complex. Furthermore, it was found that the highly purified B-TFIID fractions have (d)ATPase activity.

Immobilization of DNA via oligonucleotides containing an aldehyde or carboxylic acid group at the 5' terminus.

A general method for the immobilization of DNA through its 5'-end has been developed. A synthetic oligonucleotide, modified at its 5'-end with an aldehyde or carboxylic acid, was attached to latex microspheres containing hydrazide residues. Using T4 polynucleotide ligase and an oligonucleotide splint, a single stranded 98mer was efficiently joined to the immobilized synthetic fragment. After impregnation of the latex microspheres with the fluorescent dye, Nile Red and attachment of an aldehyde 16mer, 5 X 10(5) bead-DNA conjugates could be detected with a conventional fluorimeter.