A web services choreography scenario for interoperating bioinformatics applications

Background  

Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow.     

Chemical cross-linking and mass spectrometry for protein structural modeling

The growth of gene and protein sequence information is currently so rapid that three-dimensional structural information is lacking for the overwhelming majority of known proteins. In this review, efforts towards rapid and sensitive methods for protein structural characterization are described, complementing existing technologies. Based on chemical cross-linking and offering the analytical speed and sensitivity of mass spectrometry these methodologies are thought to contribute valuable tools towards future high throughput protein structure elucidation.     

The p53 tumour suppressor inhibits glucocorticoid-induced proliferation of erythroid progenitors

Hypoxia encountered at high altitude, blood loss and erythroleukemia instigate stress erythropoiesis, which involves glucocorticoid-induced proliferation of erythroid progenitors (ebls). The tumour suppressor p53 stimulates hematopoietic cell maturation and antagonizes glucocorticoid receptor (GR) activity in hypoxia, suggesting that it may inhibit stress erythropoiesis. We report that mouse fetal liver ebls that lack p53 proliferate better than wild-type cells in the presence of the GR agonist dexamethasone. An important mediator of GR-induced ebl self-renewal, the c-myb gene, is induced to higher levels in p53^–/– ebls by dexamethasone. The stress response to anemia is faster in the spleens of p53^–/– mice, as shown by the higher levels of colony forming units erythroids and the increase in the CD34/c-kit double positive population. Our results show that p53 antagonizes GR-mediated ebl expansion and demonstrate for the first time that p53–GR cross-talk is important in a physiological process in vivo: stress erythropoiesis.     

Transgenic rice plants expressing a Bacillus subtilis protoporphyrinogen oxidase gene are resistant to diphenyl ether herbicide oxyfluorfen

Protoporphyrinogen oxidase (Protox), the penultimate step enzyme of the branch point for the biosynthetic pathway of Chl and hemes, is the target site of action of diphenyl ether (DPE) herbicides. However, Bacillus subtilis Protox is known to be resistant to the herbicides. In order to develop the herbicide-resistant plants, the transgenic rice plants were generated via expression of B. subtilis Protox gene under ubiquitin promoter targeted to the cytoplasm or to the plastid using Agrobacterium-mediated gene transformation. The integration and expression of the transgene were investigated at T0 generation by DNA and RNA blots. Most transgenic rice plants revealed one copy transgene insertion into the rice genome, but some with 3 copies. The expression levels of B. subtilis Protox mRNA appeared to correlate with the copy number. Furthermore, the plastidal transgenic lines exhibited much higher expression of the Protox mRNA than the cytoplasmic transgenic lines. The transgenic plants expressing the B. subtilis Protox gene at T0 generation were found to be resistant to oxyfluorfen when judged by cellular damage with respect to cellular leakage, Chl loss, and lipid peroxidation. The transgenic rice plants targeted to the plastid exhibited higher resistance to the herbicide than the transgenic plants targeted to the cytoplasm. In addition, possible resistance mechanisms in the transgenic plants to DPE herbicides are discussed.     

Estimated flow resistance increase in a spiral human coronary artery segment

Coronary flow estimates were made for a spiral coronary artery segment (identified from a post-mortem replica casting) by using a modified Dean number based on the approximate coil radius of curvature, as suggested earlier. The estimates were found to correlate experimental pressure drop data for helical coiled tubes. Over a physiological range of mean Reynolds numbers from 100 to 400 for blood flow through main coronary arteries, estimates of the flow resistance increase relative to a straight lumen segment ranged from about 20 to 80 percent, and were of similar magnitude to those found in a flow study in a sinuous coronary vessel segment with no spiral.     

Cloning and Bacterial Expression of Sesquiterpene Cyclase, a Key Branch Point Enzyme for the Synthesis of Sesquiterpenoid Phytoalexin Capsidiol in UV-Challenged Leaves of Capsicum annuum

Sesquiterpene cyclase, a branch point enzyme in the generalisoprenoid pathway for the synthesis of phytoalexin capsidiol,was induced in detached leaves of Capsicum annuum (pepper) byUV treatment. The inducibility of cyclase enzyme activitiesparalleled the absolute amount of cyclase protein(s) of pepperimmunodetected by monoclonal antibodies raised against tobaccosesquiterpene cyclase. A cDNA library was constructed with poly(A)⁺RNA isolated from 24 h UV-challenged leaves of pepper. A cDNAclone for sesquiterpene cyclase in pepper was isolated by usinga tobacco 5-epi aristolochene synthase gene as a hetero-logousprobe. The predicted protein encoded by this cDNA was comprisedof 559 amino acids and had a relative molecular mass of 65,095.The primary structural information from the cDNA clone revealedthat it shared 77%, 72% and 49% identity with 5-epi aristolochene,vetispiradiene, and cadinene synthase, respectively. The enzymaticproduct catalyzed by the cDNA clone in bacteria was identifiedas 5-epi aristolochene, as judged by argentation TLC. RNA blothybridization demonstrated the induction of an mRNA consistentwith the induction of cyclase enzyme activity in UV-treatedpepper. (Received March 2, 1998; Accepted June 15, 1998)     

Pathophysiology of the Ischemic Penumbra—Revision of a Concept

1. The original concept of the ischemic penumbra surrounding a focus of dense cerebral ischemia is based on electrophysiological observations. In the cortex of baboons following middle cerebral artery occlusion, complete failure of the cortical evoked potential was observed at a cerebral blood flow (CBF) threshold level of approx. 0.15 ml/g/min—a level at which extracellular potassium ion activity was only mildly elevated. With a greater CBF decrement to the range of 0.06–0.10 ml/g/min, massive increases in extracellular potassium occurred and were associated with complete tissue infarction. Thus, the ischemic penumbra has been conceptualized as a region in which CBF reduction has exceeded the threshold for failure of electrical function but not that for membrane failure.2. Recent studies demonstrate that the penumbra as defined classically by the flow thresholds does not survive prolonged periods of ischemia. The correlation of CBF autoradiograms with diffusion-weighted MR images and the regional distribution of cerebral metabolites reveals that the ischemic core region enlarges when adjacent, formerly penumbral, areas undergo irreversible deterioration during the initial hours of vascular occlusion. At the same time, the residual penumbra becomes restricted to the periphery of the ischemic territory, and its fate may depend critically upon early therapeutic intervention.3. In the border zone of brain infarcts, marked uncoupling of local CBF and glucose utilization is consistently observed. The correlation with electrophysiological measurements shows that metabolism-flow uncoupling is associated with sustained deflections of the direct current (DC) potential resembling transient depolarizations. Such penumbral cell depolarizations, which are associated with an increased metabolic workload, induce episodes of tissue hypoxia due to the constrained collateral flow, stimulate anaerobic glycolysis leading to lactacidosis, suppress protein synthesis, and, finally, compromise energy metabolism. The frequency of their occurrence correlates with the final volume of ischemic injury. Therefore, penumbral depolarizations are regarded as a key event in the pathogenesis of ischemic brain injury. Periinfarct DC deflections can be suppressed by NMDA and non-NMDA antagonists, resulting in a significant reduction of infarct size.4. The histopathological sequelae within the penumbra consist of various degrees of scattered neuronal injury, also termed incomplete infarction. The reduction of neuronal density at the infarct border is a flow- and time-dependent event which is accompanied by an early response of glial cells. As early as 3 hr after vascular occlusion a generalized microglial activation can be detected throughout the ipsilateral cortex. Astrocytic activation is observed in the intact parts of the ischemic hemisphere from 6 hr postocclusion onward. Thus, the penumbra is a spatially dynamic brain region of limited viability which is characterized by complex pathophysiological changes involving neuronal function as well as glial activation in response to local ischemic injury.