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.     

A specific domain of Gialpha required for the transactivation of Gialpha by tubulin is implicated in the organization of cellular microtubules

G(s)alpha, G(i)alpha(1), and G(q)alpha subunits bind tubulin with high affinity, whereas transducin (G(t)alpha) does not. The interaction between tubulin and Galpha, which also involves the direct transfer of GTP from tubulin to Galpha (transactivation), is not yet fully understood. This study, using chimeras of G(i)alpha and G(t)alpha, showed that the G(i)alpha (215-295) segment converted G(t)alpha to bind to tubulin and this chimera (chimera 1) could be transactivated by tubulin. Insertion of G(t)alpha (237-270) into chimera 1 to form chimera 2 resulted in a protein that, like G(t)alpha, did not bind tubulin. Thus, it was thought that the G(i)alpha (237-270) domain was essential to modulate the binding of G(i)alpha(1) to tubulin. Surprisingly, when domain (237-270) of G(i)alpha was replaced by G(t)alpha (237-270) to form chimera 3, the chimera bound to tubulin with a similar affinity (K(D) congruent with 120 nm) as wild-type G(i)alpha(1). However, even though chimera 3 displayed normal GTP binding, it was not transactivated by GTP-tubulin. Furthermore, when these chimeras were expressed in COS-1 cells, cellular processes in cells overexpressing G(i)alpha(1) or chimera 1 were more abundant and longer than those in native cells. Galpha was seen throughout the length of the process. Morphology of cells expressing chimera 2 was identical to controls. Consistent with the role of Chimera 3 as a "dominant negative" Galpha, cells transfected with chimera 3 had only few truncated processes. This study demonstrates that although G(i)alpha (237-270) is not obligatory for the binding of G(i)alpha to tubulin, it is crucial for the transactivation of Galpha by tubulin. These results also suggest that the transactivation of Galpha by tubulin may play an important role in modulating microtubule organization and cell morphology.     

Closely related G-protein-coupled receptors use multiple and distinct domains on G-protein alpha-subunits for selective coupling

The molecular basis of selectivity in G-protein receptor coupling has been explored by comparing the abilities of G-protein heterotrimers containing chimeric Galpha subunits, comprised of various regions of Gi1alpha, Gtalpha, and Gqalpha, to stabilize the high affinity agonist binding state of serotonin, adenosine, and muscarinic receptors. The data indicate that multiple and distinct determinants of selectivity exist for individual receptors. While the A1 adenosine receptor does not distinguish between Gi1alpha and Gtalpha sequences, the 5-HT1A and 5-HT1B serotonin and M2 muscarinic receptors can couple with Gi1 but not Gt. It is possible to distinguish domains that eliminate coupling and are defined as "critical," from those that impair coupling and are defined as "important." Domains within the N terminus, alpha4-helix, and alpha4-helix-alpha4/beta6-loop of Gi1alpha are involved in 5-HT and M2 receptor interactions. Chimeric Gi1alpha/Gqalpha subunits verify the critical role of the Galpha C terminus in receptor coupling, however, the individual receptors differ in the C-terminal amino acids required for coupling. Furthermore, the EC50 for interactions with Gi1 differ among the individual receptors. These results suggest that coupling selectivity ultimately involves subtle and cooperative interactions among various domains on both the G-protein and the associated receptor as well as the G-protein concentration.     

Bacterial expression,purification, and characterization of rat kidney-type mitochondrial glutaminase

The human gene that encodes the kidney-type glutaminase (KGA) spans 84-kb, contains 19 exons, and encodes two alternatively spliced mRNAs. Various segments of the rat KGA cDNA were PCR amplified and cloned into a bacterial expression vector to determine whether the N- and C- terminal ends of the glutaminase protein were essential for activity. A recombinant glutaminase, lacking the coding sequence contained in exon 1, was found to be fully active. In contrast, proteins that lacked sequences from exons 1 and 2 and exons 1-3 were inactive. An additional construct that corresponded to the sequence encoded by exons 2-14 also retained full activity. Both of the fully active, truncated proteins were purified to apparent homogeneity using an incorporated N-terminal His(6)-tag and Ni(2+)-affinity chromatography. The K(M) values for glutamine of the native and recombinant forms of glutaminase were nearly identical. However, the two truncated forms of the glutaminase exhibit the characteristic phosphate activation profile only when dialyzed into a buffer lacking phosphate. Dialysis versus 10mM Tris-phosphate was sufficient to form an active tetramer. Thus, the deleted N-terminal sequence may contribute to the phosphate-dependent oligomerization and activation of the native glutaminase.     

Initial single-center experience with a new intracoronary stent

We investigated the safety and efficacy of the recently introduced intracoronary beStent(TM). High flexibility, zero shortening after expansion and delineating gold markers at either end of the stent are favorable features of this device. Between July 1996 and February 1997, 117 patients received a total of 126 stents, measuring 15, 25 and 35 mm in length. The majority of lesions were located in the LAD (n = 48; 38%), followed by lesions in the RCA (n = 41; 33%) and the circumflex artery (n = 28; 22%). Nine additional stents were delivered into vein grafts (7%). Successful stent deployment was achieved in 94% (n = 118), even in cases with complex lesion morphology and angulated segments. The markers proved to be helpful in placing the stent close to side-branches and whenever serial stents were used. Complications during hospitalization were as follows: one cardiac death unrelated to stenting, one subacute stent thrombosis after 30 min of effective anticoagulation and one Q-wave myocardial infarction due to peripheral thrombus embolization after stent placement in a vein graft. One patient was sent for elective CABG after an unsatisfactory procedural result. Stent loss occurred in four patients, and all stents could be retrieved successfully; in another four patients stent placement at the target site was impossible. We conclude that the investigated stent demonstrates several favorable stent characteristics which have proved to be useful in treating complex lesions by providing favorable acute results with a low complication rate.     

Tryptophan207 is involved in the GTP-dependent conformational switch in the α subunit of the G protein transducin: Chymotryptic digestion patterns of the GTPγS and GDP-bound forms

The limited proteolytic pattern of transducin,G _t , and its purified subunits with chymotrypsin were analyzed and the cleavage sites on the α _t subunit were identified. The α _t subunit in the GTPγS bound form was cleaved into a major 38 kD fragment, whereas α _t -GDP was progressively digested into 38, 23, 21, and 15 kD fragments. The βγ _t subunit was not very sensitive to proteolytic digestion with chymotrypsin. The γ _t subunit was not cleaved and only a small portion of β _t was digested into several fragments. In order to determine which proteolytic fragment of α _t still contained the carboxyl terminal region, chymotrypsinization was carried out usingG _t previously³²P-labeled at Cys³⁴⁷ by petrussis toxin-catalyzed ADP-ribosylation. The³²P-label was mainly associated with the α _t subunit and a 15 kD fragment. The 23 and 21 kD fragments were not³²P-labeled. Analysis of amino terminal sequences of 38, 21, and 15 kD proteolytic bands allowed the identification of the major cleavage sites. Chymotrypsin had two cleavage sites in the amino terminal region of α _t , at Leu¹⁵ and Leu¹⁹. Chymotrypsin removed 15–19 amino acid residues from the amino terminus of α _t , generating two peptides (38 kD) which comigrates in gel electrophoresis. Chymotrypsin also cleaved at Trp²⁰⁷ in a conformation-dependent manner. Trp²⁰⁷ of α _t -GTPγS was resistant to proteolysis but α _t -GDP and the 38 kD fragments of α _t -GDP produced the 23 and 21 kD fragments, respectively, and a 15 kD fragment containing the carboxyl terminus. This proves that the environment of Trp²⁰⁷ changes when GTP or GTPγS is bound, leading to its inaccessibility to chymotrypsin.     

The effect of a taurine-containing drink on performance in 10 endurance-athletes

Summary To determine the effect of a taurine-enriched drink Red Bull on performance, 10 endurance-athletes performed three trials. After 60 min. cycling at approximately 70% VO₂ max, the subjects pedalled to exhaustion on a cycle ergometer. During each exercise, the subjects received 500 ml of a test-drink after 30 min. submaximal cycling: Red Bull without taurine, without glucuronolacton (U1), Red Bull without taurine, without glucuronolacton, without caffeine (U2) and Red Bull original drink containing taurine, glucuronolacton and caffeine (U3).The heart rate level was significantly lower in U3 (p = 0,0031) 15 min. after application. The plasma catecholamines increased slightly from begin of exercise to 15 min. after application of the drinks in all trials but remained on a significantly lower level in U3 (epinephrine (p = 0,0011) and norepinephrine (p = 0,0003). Endurance time was significantly longer with Red Bull original in U3 (p = 0,015). The results of this study show a positive effect of a taurine-containing drink on hormonal responses which leads to a higher performance.     

Two amino acids within the alpha4 helix of Galphai1 mediate coupling with 5-hydroxytryptamine1B receptors.

We previously reported that residues 299-318 in Galphai1 participate in the selective interaction between Galphai1 and the 5-hydroxytryptamine1B (5-HT1B) receptor (Bae, H., Anderson, K., Flood, L. A., Skiba, N. P., Hamm, H. E., and Graber, S. G. (1997) J. Biol. Chem. 272, 32071-32077). The present study more precisely defines which residues within this domain are critical for 5-HT1B receptor-mediated G protein activation. A series of Galphai1/Galphat chimeras and point mutations were reconstituted with Gbetagamma and Sf9 cell membranes containing the 5-HT1B receptor. Functional coupling to 5-HT1B receptors was assessed by 1) [35S]GTPgammaS binding and 2) agonist affinity shift assays. Replacement of the alpha4 helix of Galphai1 (residues 299-308) with the corresponding sequence from Galphat produced a chimera (Chi22) that only weakly coupled to the 5-HT1B receptor. In contrast, substitution of residues within the alpha4-beta6 loop region of Galphai1 (residues 309-318) with the corresponding sequence in Galphat either permitted full 5-HT1B receptor coupling to the chimera (Chi24) or only minimally reduced coupling to the chimeric protein (Chi25). Two mutations within the alpha4 helix of Galphai1 (Q304K and E308L) reduced agonist-stimulated [35S]GTPgammaS binding, and the effects of these mutations were additive. The opposite substitutions within Chi22 (K300Q and L304E) restored 5-HT1B receptor coupling, and again the effects of the two mutations were additive. Mutations of other residues within the alpha4 helix of Galphai1 had minimal to no effect on 5-HT1B coupling behavior. These data provide evidence that alpha4 helix residues in Galphai participate in directing specific receptor interactions and suggest that Gln304 and Glu308 of Galphai1 act in concert to mediate the ability of the 5-HT1B receptor to couple specifically to inhibitory G proteins.     

Synthesis of Indole Derived Protease-Activated Receptor 4 Antagonists and Characterization in Human Platelets

Protease activated receptor-4 (PAR4) is one of the thrombin receptors on human platelets and is a potential target for the management of thrombotic disorders. We sought to develop potent, selective, and novel PAR4 antagonists to test the role of PAR4 in thrombosis and hemostasis. Development of an expedient three-step synthetic route to access a novel series of indole-based PAR4 antagonists also necessitated the development of a platelet based high-throughput screening assay. Screening and subsequent structure activity relationship analysis yielded several selective PAR4 antagonists as well as possible new scaffolds for future antagonist development.