Mining metabolites: extracting the yeast metabolome from the literature

Text mining methods have added considerably to our capacity to extract biological knowledge from the literature. Recently the field of systems biology has begun to model and simulate metabolic networks, requiring knowledge of the set of molecules involved. While genomics and proteomics technologies are able to supply the macromolecular parts list, the metabolites are less easily assembled. Most metabolites are known and reported through the scientific literature, rather than through large-scale experimental surveys. Thus it is important to recover them from the literature. Here we present a novel tool to automatically identify metabolite names in the literature, and associate structures where possible, to define the reported yeast metabolome. With ten-fold cross validation on a manually annotated corpus, our recognition tool generates an f-score of 78.49 (precision of 83.02) and demonstrates greater suitability in identifying metabolite names than other existing recognition tools for general chemical molecules. The metabolite recognition tool has been applied to the literature covering an important model organism, the yeast Saccharomyces cerevisiae, to define its reported metabolome. By coupling to ChemSpider, a major chemical database, we have identified structures for much of the reported metabolome and, where structure identification fails, been able to suggest extensions to ChemSpider. Our manually annotated gold-standard data on 296 abstracts are available as supplementary materials. Metabolite names and, where appropriate, structures are also available as supplementary materials.     

Potent cardiovascular actions of homologous adrenomedullins in eels

Adrenomedullin (AM), known as a multifunctional hormone in mammals, forms a unique family of five paralogous peptides in teleost fish. To examine their cardiovascular effects using homologous AMs in eels, we isolated cDNAs encoding four eel AMs, and named AM1 (ortholog of mammalian AM), AM2, AM3 (paralog of AM2 generated only in teleost lineage), and AM5 according to the known teleost AM sequences. Unlike pufferfish, not only AM1 but AM2/3 and AM5 were expressed ubiquitously in various eel tissues. Synthetic mature AM1, AM2, and AM5 exhibited vasodepressor effects after intra-arterial injections, and the effects were more potent at dorsal aorta than at ventral aorta. This indicates that AMs preferentially act on peripheral resistance vessels rather than on branchial arterioles. The potency was in the order of AM2 = AM5 > AM1 in both freshwater (FW) and seawater (SW) eels, which is different from the result of mammals in which AM1 is as potent as, or more potent than, AM2 when injected peripherally. The minimum effective dose of AM2 and AM5 in eels was 1/10 that of AM1 in mammals. The hypotension reached 50% at 1.0 nmol/kg of AM2 and AM5, which is much greater than atrial natriuretic peptide (20%), another potent vasodepressor hormone. Even with such hypotension, AMs did not change heart rate in eels. In addition, AM1 increased blood pressure at ventral aorta and dorsal aorta immediately after an initial hypotension at 5.0 nmol/kg, but not with AM2 and AM5. These data strongly suggest that specific receptors for AM2 and AM5 exist in eels, which differ from the AM1 receptors identified in mammals.     

Potent cardiovascular effects of homologous urotensin II (UII)-related peptide and UII in unanesthetized eels after peripheral and central injections

We cloned cDNAs encoding urotensin II (UII)-related peptide (URP) and UII in Japanese eel, Anguilla japonica, the former being the first such cloning in teleost fishes. Unlike the exclusive expression of UII in the urophysis, the URP gene was expressed most abundantly in the brain (medulla oblongata) followed by the urophysis. Peripheral injections of URP into eels increased blood pressure by 16.1 ± 0.8 mmHg at 0.1 nmol/kg in ventral aortic blood pressure (P(VA)) and with similar potency and efficacy to that of UII (relative potency of URP to UII = 0.83). URP/UII and ANG II preferentially acted on the branchial and systemic circulations, respectively, and the duration of effect was distinct among the three peptides in the order of UII (60 min) >URP (30 min) >ANG II (14 min) in P(VA). Urantide, a mammalian UII receptor antagonist, inhibited the URP effect (-63.6 ± 5.2%) to a greater extent than for UII (-39.9 ± 5.0%). URP and UII constricted isolated eel branchial and systemic arteries, showing their direct actions on the vascular smooth muscle. Central injection of URP increased blood pressure by 12.3 ± 0.8 mmHg at 50 pmol/eel in P(VA) and with similar efficacy but less potency (relative potency = 0.47) and shorter duration compared with UII. The central actions of URP/UII were more potent on the branchial circulation than on the systemic circulation, again opposite the effects of ANG II. The similar responses to peripheral and central injections suggest that peripheral hormones may act on the brain. Taken together, in eels, URP and UII are potent cardiovascular hormones like ANG II, acting directly on the peripheral vasculature, as well as a central vasomotor site, and their actions are mediated to different degrees by the UII receptor.     

In vivo airway eosinophil accumulation does not enhance antigen- or propranolol-induced bronchoconstriction in guinea pigs

BACKGROUND: Chronic airway eosinophil accumulation is characteristic of asthma. However, it remains unclear whether airway eosinophils enhance or reduce release of chemical mediators and/or action of the released mediators in the airways in vivo, because previous investigators have indicated that eosinophil-derived factors such as histaminase and arylsulfatase may alter the allergic reaction by metabolizing chemical mediators. Recently, we have developed a guinea pig model of propranolol-induced bronchoconstriction (PIB), which is mediated by lipid mediators such as thromboxane A2 (TxA2), cysteinyl leukotrienes (cLTs) and platelet activation factor (PAF). This study was conducted to explain the influence of airway eosinophil accumulation on antigen-induced bronchoconstriction and the following PIB, both of which are mediated by lipid mediators. METHODS: Guinea pigs were transnasally treated with 75 microg/kg of polymyxin-B or vehicle twice a week for a total of 3 weeks. Guinea pigs were anesthetized and treated with diphenhydramine hydrochloride, and then artificially ventilated 24 h after the last administration of polymyxin-B or vehicle followed by passive sensitization. Propranolol at a concentration of 10 mg/ml was inhaled 20 min after an aerosolized antigen challenge. RESULTS: The proportion of eosinophils in bronchoalveolar lavage fluid obtained 15 min after the propranolol inhalation was significantly increased in guinea pigs treated with polymyxin-B compared with the vehicle. The polymyxin-B treatment did not affect antigen-induced bronchoconstriction or the following PIB. CONCLUSIONS: We conclude that eosinophils accumulated in the airways by polymyxin-B does not affect release of chemical mediators induced by antigen or propranolol inhalation, or action of released mediators in vivo.     

Evolutionary implication of the absence of atrial natriuretic peptide (ANP) in euryhaline Oryzias fishes

The genus Oryzias contains nearly 20 species, including the Japanese medaka (Oryzias latipes). Because each species exhibits different adaptability to environmental salinity, Oryzias fishes offer unique opportunities for comparative studies. To understand the mechanisms of osmotic adaptation, we are studying the functional evolution of the natriuretic peptide (NP) family??a group of small peptide hormones involved in body fluid regulation??by using Oryzias fishes. Analysis of the Japanese medaka genome revealed that 7 NP subtypes, namely, Atrial NP (ANP), B-type NP (BNP), Ventricular NP (VNP), and 4?C-type NPs (CNP-1 through CNP-4) were generated from a CNP-4-like ancestral gene discovered in the cyclostomes before the ray-finned fish/lobe-finned fish divergence. This evolutionary history has been confirmed by the discovery of hidden NP genes in tetrapods. Through analyses of phylogenetic distribution of NP subtypes, we also found that specific losses of subtypes have occurred in each vertebrate lineage. For example, ANP is absent in the Japanese and Indian medaka and the flying fish, suggesting that loss of the ANP gene occurred after the divergence of Beloniformes from Cyprinodontiformes. This fact also supports the inclusion of Oryzias into Beloniformes as suggested by phylogenetic analysis using whole mitochondrial genome sequences. How Oryzias fishes have retained their euryhalinity with a reduced number of NPs is an interesting question. CNP-3, which is functionally flexible, may be a substitute for the lost cardiac NPs.     

Relative antidipsogenic potencies of six homologous natriuretic peptides in eels

Atrial natriuretic peptide (ANP) exhibits a potent antidipsogenic effect in seawater (SW) eels to limit excess Na(+) uptake, thereby effectively promoting SW adaptation. Recently, cardiac ANP, BNP and VNP and brain CNP1, 3 and 4, have been identified in eels. We examined the antidipsogenic effect of all homologous NPs using conscious, cannulated eels in both FW and SW together with parameters that affect drinking. A dose-response study (0.01-1 nmol/kg) in SW eels showed the relative potency of the antidipsogenic effect was in the order ANP ≥ VNP > BNP = CNP3 > CNP1 ≥ CNP4, while the order was ANP = VNP = BNP > CNP3 = CNP1 = CNP4 for the vasodepressor effect. The minimum effective dose of ANP for the antidipsogenic effect is much lower than that in mammals. ANP, BNP and VNP at 0.3 nmol/kg decreased drinking, plasma Na(+) concentration and aortic pressure and increased hematocrit in SW eels. The cardiac NPs induced similar changes in drinking, aortic pressure and hematocrit in FW eels, but aside from BNP no change in plasma Na(+) concentration. CNPs had no effect on drinking, plasma Na(+) concentration and hematocrit but induced mild hypotension in both FW and SW eels, except for CNP3 that inhibited drinking in SW eels. These results show that ANP, BNP and VNP are potent antidipsogenic hormones in eels in spite of other regulatory factors working to induce drinking, and that CNPs are without effects on drinking except for the ancestor of the cardiac NPs, CNP3.     

In vivo PAF-induced airway eosinophil accumulation reduces bronchial responsiveness to inhaled histamine

Chronic eosinophilic bronchitis and bronchial hyperresponsiveness have been considered to be the fundamental features of bronchial asthma. However, the role of airway eosinophils in bronchial responsiveness in vivo has not been fully discussed. The aim of this study was to investigate the direct effect of airway eosinophil accumulation on bronchial responsiveness in vivo. Guinea pigs were transnasally treated with platelet activating factor (PAF) or vehicle twice a week for a total of 3 weeks. Anesthetized guinea pigs were surgically cannulated and artificially ventilated 48 h after the last administration of PAF or vehicle. Ten minutes after the installation of artificial ventilation, ascending doses of histamine were inhaled. In a subsequent study, selective inhibitors of diamine oxidase and histamine N-methyltransferase were intravenously administered before the histamine inhalation in the PAF-treated animals. Next study was conducted 20 min after treatment with indomethacin in this study line. Finally, ascending doses of methacholine were inhaled in our animal model. Proportion of eosinophils and the number of nuclear segmentation in bronchoalveolar lavage fluid significantly increased in guinea pigs treated with PAF compared with vehicle and this finding was confirmed histologically. Nevertheless, bronchial responsiveness to inhaled histamine, but not methacholine, was significantly decreased by the PAF treatment. This bronchoprotective effect induced by PAF remained following aminoguanidine and histamine N-methyltransferase administration, but abolished by treatment of indomethacin. These results suggest that in vivo airway eosinophils may reduce nonspecific bronchial responsiveness through production of inhibitory or bronchoprotective prostanoids, but not through histaminase production.     

Condition factor dependency of burst swimming ability between wild and hatchery-reared chum salmon fry (Oncorhynchus keta)

Ichthyological Research - Burst swimming velocity (Uburst) was compared between wild and hatchery-reared chum salmon fry. In the hatchery-reared fry, Uburst was significantly correlated with the...     

The area postrema in hindbrain is a central player for regulation of drinking behavior in Japanese eels

It is recognized that fish will drink the surrounding water by reflex swallowing without a thirst sensation. We evaluated the role of the area postrema (AP), a sensory circumventricular organ (CVO) in the medulla oblongata, in the regulation of drinking behavior of seawater (SW) eels. The antidipsogenic effects of ghrelin and atrial natriuretic peptide and hypervolemia and hyperosmolemia (1 M sucrose or 10% NaCl) as well as the dipsogenic effects of angiotensin II and hypovolemia (hemorrhage) were profoundly diminished after AP lesion (APx) in eels compared with sham controls. However, the antidipsogenic effect of urotensin II was not influenced by APx, possibly due to the direct baroreflex inhibition on the swallowing center in eels. When ingested water was drained via an esophageal fistula, water intake increased 30-fold in sham controls but only fivefold in APx eels, suggesting a role for the AP in continuous regulation of drinking by SW eels. After transfer from freshwater to SW, APx eels responded normally with an immediate burst of drinking, but after 4 wk these animals showed a much greater increase in plasma osmolality than controls, suggesting that the AP is involved in acclimation to SW by fine tuning of the drinking rate. Taken together, the AP in the hindbrain of eels plays an integral role in SW acclimation, acting as a conduit of information from plasma for the regulation of drinking, probably without a thirst sensation. This differs from mammals in which sensory CVOs in the forebrain play pivotal roles in thirst regulation.     

Potent osmoregulatory actions of homologous adrenomedullins administered peripherally and centrally in eels

The teleost adrenomedullin (AM) family consists of three groups, AM1/AM4, AM2/AM3, and AM5. In the present study, we examined the effects of homologous AM1, AM2, and AM5 on drinking and renal function after peripheral or central administration in conscious freshwater eels. AM2 and AM5, but not AM1, exhibited dose-dependent (0.01-1 nmol/kg) dipsogenic and antidiuretic effects after intra-arterial bolus injection. The antidiuretic effect was significantly correlated with the degree of associated hypotension. To avoid the potential indirect osmoregulatory effects of AM-induced hypotension, infusion of AMs was also performed at nondepressor doses. Drinking was enhanced dose-dependently at 0.1-3 pmol.kg(-1).min(-1) of AM2 and AM5, matching the potency and efficacy of angiotensin II (ANG II), the most potent dipsogenic hormone known thus far. AM2 and AM5 infusion also induced mild antidiuresis, while AM1 caused antinatriuresis. Additionally, AMs were injected into the third and fourth ventricles of conscious eels to assess their site of dipsogenic action. However, none of the AMs at 0.05-0.5 nmol induced drinking, while ANG II was highly dipsogenic. AM2 and ANG II injected into the third ventricle increased arterial pressure while AM5 decreased it in a dose-dependent manner, and both AM2 and AM5 decreased blood pressure when injected into the fourth ventricle. These data suggest that circulating AM2 and AM5 act on a target site in the brain that lacks the blood-brain barrier. Collectively, the present study showed that AM2 and AM5 are potent osmoregulatory hormones in the eel, and their actions imply involvement in seawater adaptation of this euryhaline species.