The genome sequence of the Loggerhead sea turtle, Caretta caretta Linnaeus 1758.

We present a genome assembly of Caretta caretta (the Loggerhead sea turtle; Chordata, Testudines, Cheloniidae), generated from genomic data from two unrelated females. The genome sequence is 2.13 gigabases in size. The assembly has a busco completion score of 96.1% and N50 of 130.95 Mb. The majority of the assembly is scaffolded into 28 chromosomal representations with a remaining 2% of the assembly being excluded from these.

Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes.

Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. Here, we present and compare the genomes of four different North American spruces: the genome assemblies for Engelmann spruce (Picea engelmannii) and Sitka spruce (Picea sitchensis) together with improved and more contiguous genome assemblies for white spruce (Picea glauca) and for a naturally occurring introgress of these three species known as interior spruce (P. engelmannii × glauca × sitchensis). The genomes were structurally similar, and a large part of scaffolds could be anchored to a genetic map. The composition of the interior spruce genome indicated asymmetric contributions from the three ancestral genomes. Phylogenetic analysis of the nuclear and organelle genomes revealed a topology indicative of ancient reticulation. Different patterns of expansion of gene families among genomes were observed and related with presumed diversifying ecological adaptations. We identified rapidly evolving genes that harbored high rates of non-synonymous polymorphisms relative to synonymous ones, indicative of positive selection and its hitchhiking effects. These gene sets were mostly distinct between the genomes of ecologically contrasted species, and signatures of convergent balancing selection were detected. Stress and stimulus response was identified as the most frequent function assigned to expanding gene families and rapidly evolving genes. These two aspects of genomic evolution were complementary in their contribution to divergent evolution of presumed adaptive nature. These more contiguous spruce giga-genome sequences should strengthen our understanding of conifer genome structure and evolution, as their comparison offers clues into the genetic basis of adaptation and ecology of conifers at the genomic level. They will also provide tools to better monitor natural genetic diversity and improve the management of conifer forests. The genomes of four closely related North American spruces indicate that their high similarity at the morphological level is paralleled by the high conservation of their physical genome structure. Yet, the evidence of divergent evolution is apparent in their rapidly evolving genomes, supported by differential expansion of key gene families and large sets of genes under positive selection, largely in relation to stimulus and environmental stress response.

Improved structural variant interpretation for hereditary cancer susceptibility using long-read sequencing.

PURPOSE: Structural variants (SVs) may be an underestimated cause of hereditary cancer syndromes given the current limitations of short-read next-generation sequencing. Here we investigated the utility of long-read sequencing in resolving germline SVs in cancer susceptibility genes detected through short-read genome sequencing. METHODS: Known or suspected deleterious germline SVs were identified using Illumina genome sequencing across a cohort of 669 advanced cancer patients with paired tumor genome and transcriptome sequencing. Candidate SVs were subsequently assessed by Oxford Nanopore long-read sequencing. RESULTS: Nanopore sequencing confirmed eight simple pathogenic or likely pathogenic SVs, resolving three additional variants whose impact could not be fully elucidated through short-read sequencing. A recurrent sequencing artifact on chromosome 16p13 and one complex rearrangement on chromosome 5q35 were subsequently classified as likely benign, obviating the need for further clinical assessment. Variant configuration was further resolved in one case with a complex pathogenic rearrangement affecting TSC2. CONCLUSION: Our findings demonstrate that long-read sequencing can improve the validation, resolution, and classification of germline SVs. This has important implications for return of results, cascade carrier testing, cancer screening, and prophylactic interventions.

Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes.

Advanced and metastatic tumors with complex treatment histories drive cancer mortality. Here we describe the POG570 cohort, a comprehensive whole-genome, transcriptome and clinical dataset, amenable for exploration of the impacts of therapies on genomic landscapes. Previous exposure to DNA-damaging chemotherapies and mutations affecting DNA repair genes, including POLQ and genes encoding Polζ, were associated with genome-wide, therapy-induced mutagenesis. Exposure to platinum therapies coincided with signatures SBS31 and DSB5 and, when combined with DNA synthesis inhibitors, signature SBS17b. Alterations in ESR1, EGFR, CTNNB1, FGFR1, VEGFA and DPYD were consistent with drug resistance and sensitivity. Recurrent noncoding events were found in regulatory region hotspots of genes including TERT, PLEKHS1, AP2A1 and ADGRG6. Mutation burden and immune signatures corresponded with overall survival and response to immunotherapy. Our data offer a rich resource for investigation of advanced cancers and interpretation of whole-genome and transcriptome sequencing in the context of a cancer clinic.

The Genome of the Steller Sea Lion (Eumetopias jubatus).

The Steller sea lion is the largest member of the Otariidae family and is found in the coastal waters of the northern Pacific Rim. Here, we present the Steller sea lion genome, determined through DNA sequencing approaches that utilized microfluidic partitioning library construction, as well as nanopore technologies. These methods constructed a highly contiguous assembly with a scaffold N50 length of over 14 megabases, a contig N50 length of over 242 kilobases and a total length of 2.404 gigabases. As a measure of completeness, 95.1% of 4104 highly conserved mammalian genes were found to be complete within the assembly. Further annotation identified 19,668 protein coding genes. The assembled genome sequence and underlying sequence data can be found at the National Center for Biotechnology Information (NCBI) under the BioProject accession number PRJNA475770.

The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis.

The grizzly bear (Ursus arctos ssp. horribilis) represents the largest population of brown bears in North America. Its genome was sequenced using a microfluidic partitioning library construction technique, and these data were supplemented with sequencing from a nanopore-based long read platform. The final assembly was 2.33 Gb with a scaffold N50 of 36.7 Mb, and the genome is of comparable size to that of its close relative the polar bear (2.30 Gb). An analysis using 4104 highly conserved mammalian genes indicated that 96.1% were found to be complete within the assembly. An automated annotation of the genome identified 19,848 protein coding genes. Our study shows that the combination of the two sequencing modalities that we used is sufficient for the construction of highly contiguous reference quality mammalian genomes. The assembled genome sequence and the supporting raw sequence reads are available from the NCBI (National Center for Biotechnology Information) under the bioproject identifier PRJNA493656, and the assembly described in this paper is version QXTK01000000.

Effects of high fructose intake on the development of hypertension in the spontaneously hypertensive rats: the role of AT1R/gp91PHOX signaling in the rostral ventrolateral medulla.

Both genetic and dietary factors determine the development of hypertension. Whether dietary factor impacts the development of hereditary hypertension is unknown. Here, we evaluated the effect of daily high-fructose diet (HFD) on the development of hypertension in adolescent spontaneously hypertensive rats (SHR). Six-week-old SHR were randomly divided into two groups to receive HFD or normal diet (ND) for 3 weeks. The temporal profile of systolic blood pressure, alongside the sympathetic vasomotor activity, in the SHR-HFD showed significantly greater increases at 9-12 weeks of age compared with the age-matched SHR-ND group. Immunofluorescence was used to identify the distribution of reactive oxygen species (ROS), oxidants and antioxidants in rostral ventrolateral medulla (RVLM) where sympathetic premotor neurons reside. In RVLM of SHR-HFD, the levels of ROS accumulation and lipid peroxidation were elevated. The changes in protein expression were measured by Western blot. NADPH oxidase subunit gp91phox and angiotensin II type I receptor were up-regulated in RVLM neuron. On the other hand, the expression of extracellular superoxide dismutase was suppressed. Both molecular and hemodynamic changes in the SHR-HFD were rescued by oral pioglitazone treatment from weeks 7 to 9. Furthermore, central infusion with tempol, a ROS scavenger, effectively ameliorated ROS accumulation in RVLM and diminished the heightened pressor response and enhanced sympathetic activity in the SHR-HFD. Together, these results suggest that HFD intake at adolescent SHR may impact the development of hypertension via increasing oxidative stress in RVLM which could be effectively attenuated by pioglitazone treatment.

Attenuation of Isoflurane Preconditioning-Induced Acute Cardioprotection in Hypertensive Hypertrophied Hearts.

OBJECTIVES: To evaluate the efficiency of isoflurane-induced anesthetic preconditioning and the role of mitochondrial manganese superoxide dismutase (MnSOD) in hypertensive hypertrophied hearts. DESIGN: A prospective animal investigation. SETTING: Medical center hospital research laboratory. PARTICIPANTS: Male spontaneously hypertensive rats (SHRs) and normotensive control Wistar-Kyoto (WKY) rats. INTERVENTIONS: All pentobarbital-anesthetized open-chest rats were subjected to a 45-minute left coronary artery occlusion followed by a 120-minute reperfusion. Before ischemia, both SHR and WKY rats were assigned randomly to receive a 30-minute exposure to 0.9% saline or 1.0 minimum alveolar concentration isoflurane. MEASUREMENTS AND MAIN RESULTS: The myocardial infarct size, assessed as a percentage of the area at risk, was significantly greater in the hypertrophied SHRs than in the WKY rats (65.3%±8.7% v 51.8%±7.2%, p<0.05). Isoflurane preconditioning appreciably reduced the infarct size in the WKY hearts (30.9%±10.5%, p<0.05) but not in the SHR hearts. MnSOD protein expression and enzymatic activity were increased drastically in response to isoflurane exposure in the hearts of the WKY rats (p<0.05) but not in the SHRs. CONCLUSIONS: Isoflurane-induced anesthetic preconditioning is attenuated in hypertensive hypertrophied hearts. This impairment may be associated with the loss of MnSOD augmentation during ischemia and reperfusion.

Nontranscriptional activation of PI3K/Akt signaling mediates hypotensive effect following activation of estrogen receptor ß in the rostral ventrolateral medulla of rats.

BACKGROUND: Estrogen acts on the rostral ventrolateral medulla (RVLM), where sympathetic premotor neurons are located, to elicit vasodepressor effects via an estrogen receptor (ER)ß-dependent mechanism. We investigated in the present study nontranscriptional mechanism on cardiovascular effects following activation of ERß in the RVLM, and delineated the involvement of phosphatidylinositol 3-kinase (PI3K)/serine/threonine kinase (Akt) signaling pathway in the effects. METHODS: In male Sprague-Dawley rats maintained under propofol anesthesia, changes in arterial pressure, heart rate and sympathetic neurogenic vasomotor tone were examined after microinjection bilaterally into RVLM of 17ß-estradiol (E2ß) or a selective ERα or ERß agonist. Involvement of ER subtypes and PI3K/Akt signaling pathway in the induced cardiovascular effects were studied using pharmacological tools of antagonists or inhibitors, gene manipulation with antisense oligonucleotide (ASON) or adenovirus-mediated gene transfection. RESULTS: Similar to E2ß (1 pmol), microinjection of ERß agonist, diarylpropionitrile (DPN, 1, 2 or 5 pmol), into bilateral RVLM evoked dose-dependent hypotension and reduction in sympathetic neurogenic vasomotor tone. These vasodepressive effects of DPN (2 pmol) were inhibited by ERß antagonist, R,R-tetrahydrochrysene (50 pmol), ASON against ERß mRNA (250 pmol), PI3K inhibitor LY294002 (5 pmol), or Akt inhibitor (250 pmol), but not by ERα inhibitor, methyl-piperidino-pyrazole (1 nmol), or transcription inhibitor, actinomycin D (5 or 10 nmol). Gene transfer by microinjection into bilateral RVLM of adenovirus encoding phosphatase and tensin homologues deleted on chromosome 10 (5 × 10(8) pfu) reversed the vasodepressive effects of DPN. CONCLUSIONS: Our results indicate that vasodepressive effects following activation of ERß in RVLM are mediated by nongenomic activation of PI3K/Akt signaling pathway. This study provides new insight in the intracellular signaling cascades involved in central vasodepressive functions of estrogen.

Autonomic nervous system and nitric oxide in antihypertensive and cardiac inhibitory effects induced by red mold rice in spontaneously hypertensive rats.

The aim of this study was to investigate the antihypertensive activity of the ethanol extract (EE) of red mold rice (RMR) and to explore its mechanism of action. In comparison to EE of nonfermented rice, the EE of RMR contained higher levels of total phenolic, total flavonoids, gamma-aminobutyric acid, and monacolin K. Intravenous bolus administration of the EE (10-50 mg/kg) resulted in biphasic, dose-dependent antihypertensive effects and decreases in heart rate, cardiac contractility, and sympathetic vasomotor tone in spontaneously hypertensive rats. The initial and delayed antihypertensive responses, and the negative inotropic and chronotropic effects of EE treatment (30 mg/kg, i.v.) were significantly reduced by pretreatment with hexamethonium (30 mg/kg, i.v.) and N(G)-nitro-l-arginine methyl ester (20 mg/kg, i.v.). Pretreatment with methylatropine (1 mg/kg, i.v.), however, reversed the initial but not the delayed bradycardiac and negative inotropic effects of EE. We conclude that systemic administration of the EE of RMR elicited both transient and delayed antihypertensive actions that were mediated by the withdrawal of sympathetic tone and the production of nitric oxide (NO). The negative inotropic and chronotropic effects of EE may result from a direct sympathetic inhibition of the heart as well as an activation of the NO-dependent pathway.

Activation of nitric oxide/cGMP/PKG signaling cascade mediates antihypertensive effects of Muntingia calabura in anesthetized spontaneously hypertensive rats.

We previously reported that the leaf extract of Muntingia calabura L. (Tiliaceae) exerts a potent hypotensive effect in the normotensive rats. The antihypertensive activity of this plant extract, however, is currently unknown. In the present study, we investigated the antihypertensive effects of the n-butanol soluble fraction (BSF) from methanol leaf extract of M. calabura in spontaneously hypertensive rats (SHR), and delineated is underlying mechanisms. The intravenous bolus administration of the BSF (10-100 mg/kg) of M. calabura produced biphasic dose-related antihypertensive and bradycardiac effects in SHR. The BSF-induced initial cardiovascular depressive effects lasted for 10 min, and the delayed effects commenced 40 min and lasted for at least 120 min postinjection. These cardiovascular depressive effects of BSF treatments were greater in SHR than in normotensive Wistar-Kyoto (WKY) rats. Both the initial and delayed antihypertensive and bradycardiac effects of BSF (25 mg/kg, i.v.) in SHR, were significantly blocked by pretreatment with a nonselective nitric oxide (NO) synthase (NOS) inhibitor, a soluble guanylyl cyclase (sGC) inhibitor, or a protein kinase G (PKG) inhibitor. Moreover, the initial effects of BSF in SHR were inhibited by pretreatment with a selective endothelial NOS (eNOS) inhibitor; whereas the delayed effects were attenuated by a selective inducible NOS (iNOS) inhibitor. These results indicate that the BSF from the leaf of M. calabura elicited both transient and delayed antihypertensive and bradycardiac actions in SHR, which might be mediated through NO generated respectively by eNOS and iNOS. Furthermore, activation of sGC/cGMP/PKG signaling pathway may participate in the M. calabura-induced biphasic cardiovascular effects.

Activation of estrogen receptor beta-dependent nitric oxide signaling mediates the hypotensive effects of estrogen in the rostral ventrolateral medulla of anesthetized rats.

BACKGROUND: Apart from their well-known peripheral cardiovascular effects, emerging evidence indicates that estrogen acts as a modulator in the brain to regulate cardiovascular functions. The underlying mechanisms of estrogen in central cardiovascular regulation, however, are poorly understood. The present study investigated the cardiovascular effects of 17beta-estradiol (E2beta) in the rostral ventrolateral medulla (RVLM), where sympathetic premotor neurons are located, and delineated the engagement of nitric oxide (NO) in E2beta-induced cardiovascular responses. METHODS: In male Sprague-Dawley rats maintained under propofol anesthesia, the changes of blood pressure, heart rate and sympathetic vasomotor tone after microinjection bilaterally into the RVLM of a synthetic estrogen, E2beta were examined for at least 120 min. The involvement of ERalpha and/or ERbeta subtypes was determined by microinjection of selective ERalpha or ERbeta agonist into bilateral RVLM. Different NO synthase (NOS) inhibitors were used to evaluate the involvement of differential of NOS isoforms in the cardiovascular effects of E2beta. RESULTS: Bilateral microinjection of E2beta (0.5, 1, or 5 pmol) into the RVLM dose-dependently decreased systemic arterial pressure (SAP) and the power density of the vasomotor components of SAP signals, our experimental index for sympathetic neurogenic vasomotor tone. These cardiovascular depressive effects of E2beta (1 pmol) were abolished by co-injection of ER antagonist ICI 182780 (0.25 or 0.5 pmol), but not a transcription inhibitor actinomycin D (10 nmol). Like E2beta, microinjection bilaterally into the RVLM of a selective ERbeta agonist 2,3-bis(4-hydroxyphenyl) propionitrile (DPN, 1, 2, or 5 pmol) induced significant decreases in these hemodynamic parameters in a dose-dependent manner. In contrast, the selective ERalpha agonist 1,3,5-tris(4-hydroxyphenyl)-4-propyl-1H-pyrazole (5 pmol) did not influence the same cardiovascular parameters. Co-administration bilaterally into the RVLM of NOS inhibitor NG-nitro-L-arginine methyl ester (5 nmol) or selective inducible NOS (iNOS) inhibitor S-methylisothiourea (25 pmol), but not selective neuronal NOS inhibitor 7-nitroindazole (0.5 pmol) or endothelial NOS inhibitor N5-(1-Iminoethyl)-L-ornithine (2.5 pmol), significantly attenuated the cardiovascular depressive effects elicited by DPN (2 pmol). CONCLUSION: Our results indicate that E2beta in the RVLM elicited short-term cardiovascular depressive effects via an ERbeta-dependent nontranscriptional mechanism. These vasodepressor effects of E2beta are likely to be mediated by the iNOS-derived NO in the RVLM.

HMDB: a knowledgebase for the human metabolome.

The Human Metabolome Database (HMDB, http://www.hmdb.ca) is a richly annotated resource that is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. Since its first release in 2007, the HMDB has been used to facilitate the research for nearly 100 published studies in metabolomics, clinical biochemistry and systems biology. The most recent release of HMDB (version 2.0) has been significantly expanded and enhanced over the previous release (version 1.0). In particular, the number of fully annotated metabolite entries has grown from 2180 to more than 6800 (a 300% increase), while the number of metabolites with biofluid or tissue concentration data has grown by a factor of five (from 883 to 4413). Similarly, the number of purified compounds with reference to NMR, LC-MS and GC-MS spectra has more than doubled (from 380 to more than 790 compounds). In addition to this significant expansion in database size, many new database searching tools and new data content has been added or enhanced. These include better algorithms for spectral searching and matching, more powerful chemical substructure searches, faster text searching software, as well as dedicated pathway searching tools and customized, clickable metabolic maps. Changes to the user-interface have also been implemented to accommodate future expansion and to make database navigation much easier. These improvements should make the HMDB much more useful to a much wider community of users.

Autonomic nervous system mediates the cardiovascular effects of Rhodiola sacra radix in rats.

ETHNOPHARMACOLOGICAL RELEVANCE: Rhodiola sacra (Crassulaceae) exhibits cardiovascular bioactivities and is used in Tibetan medicine for promoting circulation and preventing hypertension. However, the underlying mechanisms of its cardiovascular effects are poorly understood. AIM OF THE STUDY: The aim of this study was therefore to evaluate the cardiovascular activity of water-soluble fraction (WtF) and n-butanol-soluble fraction (BtF) of Rhodiola sacra radix and to explore its mechanism of action in propofol anesthetized Sprague-Dawley rats. MATERIALS AND METHODS: The changes of blood pressure, heart rate and cardiac contractility after systemic administration of the extracts (10-75 mg/kg) were examined for at least 40 min. Different antagonists were used to evaluate the mechanisms of cardiovascular effects of the extracts. RESULTS: Intravenous injection of the WtF (10, 25, 35, 50 or 75 mg/kg) exhibited dose-dependent hypotension and increases in heart rate and cardiac contractility. In contrast, mild alterations in the same cardiovascular parameters were detected only at high dose (75 mg/kg) BtF. The WtF-induced hypotensive, positive inotropic and chronotropic effects were significantly abolished by pretreatment with hexamethonium (30 mg/kg, i.v.) or reserpine (5 mg/kg, i.v.), whereas the hypotensive, but not the positive inotropic or chronotropic effect was potentiated by captopril (2.5 mg/kg, i.v.). Pretreatment with methylatropine (1 mg/kg, i.v.), on the other hand, reversed the positive inotropic and chronotropic but not the hypotensive effects of WtF. The WtF-induced cardiovascular responses were not affected in rats pretreated with N(G)-nitro-l-arginine methyl ester (20 mg/kg, i.v.). CONCLUSIONS: We conclude that systemic administration of the WtF of Rhodiola sacra radix elicited a potent hypotensive effect that was mediated by the withdrawal of sympathetic vasomotor tone and interaction with the circulatory angiotensin system. The positive inotropic and chronotropic effects of WtF may result from a direct vagal inhibition on the heart.

PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites.

A particular challenge in biomedical text mining is to find ways of handling 'comprehensive' or 'associative' queries such as 'Find all genes associated with breast cancer'. Given that many queries in genomics, proteomics or metabolomics involve these kind of comprehensive searches we believe that a web-based tool that could support these searches would be quite useful. In response to this need, we have developed the PolySearch web server. PolySearch supports >50 different classes of queries against nearly a dozen different types of text, scientific abstract or bioinformatic databases. The typical query supported by PolySearch is 'Given X, find all Y's' where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. PolySearch also exploits a variety of techniques in text mining and information retrieval to identify, highlight and rank informative abstracts, paragraphs or sentences. PolySearch's performance has been assessed in tasks such as gene synonym identification, protein-protein interaction identification and disease gene identification using a variety of manually assembled 'gold standard' text corpuses. Its f-measure on these tasks is 88, 81 and 79%, respectively. These values are between 5 and 50% better than other published tools. The server is freely available at http://wishart.biology.ualberta.ca/polysearch.

The human cerebrospinal fluid metabolome.

With continuing improvements in analytical technology and an increased interest in comprehensive metabolic profiling of biofluids and tissues, there is a growing need to develop comprehensive reference resources for certain clinically important biofluids, such as blood, urine and cerebrospinal fluid (CSF). As part of our effort to systematically characterize the human metabolome we have chosen to characterize CSF as the first biofluid to be intensively scrutinized. In doing so, we combined comprehensive NMR, gas chromatography-mass spectrometry (GC-MS) and liquid chromatography (LC) Fourier transform-mass spectrometry (FTMS) methods with computer-aided literature mining to identify and quantify essentially all of the metabolites that can be commonly detected (with today's technology) in the human CSF metabolome. Tables containing the compounds, concentrations, spectra, protocols and links to disease associations that we have found for the human CSF metabolome are freely available at http://www.csfmetabolome.ca.

DrugBank: a knowledgebase for drugs, drug actions and drug targets.

DrugBank is a richly annotated resource that combines detailed drug data with comprehensive drug target and drug action information. Since its first release in 2006, DrugBank has been widely used to facilitate in silico drug target discovery, drug design, drug docking or screening, drug metabolism prediction, drug interaction prediction and general pharmaceutical education. The latest version of DrugBank (release 2.0) has been expanded significantly over the previous release. With approximately 4900 drug entries, it now contains 60% more FDA-approved small molecule and biotech drugs including 10% more 'experimental' drugs. Significantly, more protein target data has also been added to the database, with the latest version of DrugBank containing three times as many non-redundant protein or drug target sequences as before (1565 versus 524). Each DrugCard entry now contains more than 100 data fields with half of the information being devoted to drug/chemical data and the other half devoted to pharmacological, pharmacogenomic and molecular biological data. A number of new data fields, including food-drug interactions, drug-drug interactions and experimental ADME data have been added in response to numerous user requests. DrugBank has also significantly improved the power and simplicity of its structure query and text query searches. DrugBank is available at http://www.drugbank.ca.

New dihydrochalcones and anti-platelet aggregation constituents from the leaves of Muntingia calabura.

Two new dihydrochalcones, 2,3-dihydroxy-4,3',4',5'-tetramethoxydihydrochalcone (1) and 4,2',4'-trihydroxy-3'-methoxydihydrochalcone (2), and a new flavanone, (2R,3R)-(-)-3,5-dihydroxy-6,7-dimethoxyflavanone (3), together with nineteen known compounds have been isolated from the leaves of Muntingia calabura. The structures of three new compounds were determined through spectral analyses including extensive 2D-NMR data. Among the isolates, 2,3-dihydroxy-4,3',4',5'-tetramethoxydihydrochalcone, 5,7-dihydroxy-3-methoxyflavone, 5,7-dihydroxy-6-methoxyflavone, 5,4'-dihydroxy-3,7-dimethoxyflavone, (2S)-7,8,3',4',5'-pentamethoxyflavan, (2S)-5'-hydroxy-7,8,3',4'-tetramethoxyflavan, and methyl gallate exhibited significant anti-platelet aggregation activity in vitro.

HMDB: the Human Metabolome Database.

The Human Metabolome Database (HMDB) is currently the most complete and comprehensive curated collection of human metabolite and human metabolism data in the world. It contains records for more than 2180 endogenous metabolites with information gathered from thousands of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the HMDB also contains an extensive collection of experimental metabolite concentration data compiled from hundreds of mass spectra (MS) and Nuclear Magnetic resonance (NMR) metabolomic analyses performed on urine, blood and cerebrospinal fluid samples. This is further supplemented with thousands of NMR and MS spectra collected on purified, reference metabolites. Each metabolite entry in the HMDB contains an average of 90 separate data fields including a comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, biofluid concentrations, disease associations, pathway information, enzyme data, gene sequence data, SNP and mutation data as well as extensive links to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided. The HMDB is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. The HMDB is available at: www.hmdb.ca.

Activation of nitric oxide signaling pathway mediates hypotensive effect of Muntingia calabura L. (Tiliaceae) leaf extract.

The cardiovascular effect of the crude methanol extract from the leaf of Muntingia calabura L. (Tiliaceae) was investigated in the anesthetized rats. The crude methanol extract was sequentially fractionated to obtain the water-soluble extract (WSE). Intravenous administration of the WSE (10, 25, 50, 75 or 100 mg/kg) produced an initial followed by a delayed decrease in systemic arterial pressure (SAP) in a dose-dependent manner. The M. calabura-induced initial hypotension lasted for 10 min and the delayed depressor effect commenced after 90 min and lasted for at least 180 min post-injection. The same treatment, on the other hand, had no appreciable effect on heart rate (HR) or the blood gas/electrolytes concentrations. Both the initial and delayed hypotensive effects of WSE (50 mg/kg, i.v.) were significantly blocked by pre-treatment with a nonselective nitric oxide (NO) synthase (NOS) inhibitor, N(G)-nitro-L-arginine methyl ester ((L)-NAME, 0.325 mg/kg/min for 5 min) or a soluble guanylate cyclase (sGC) inhibitor, 1H-[1,2,4]oxadiazole[4,3-alpha]quinoxalin-1-one (ODQ, 0.2 mg/kg/min for 5 min). Moreover, whereas the initial depressor effect of WSE was inhibited by pre-treatment with a selective endothelial NOS (eNOS) inhibitor, N5-(1-Iminoethyl)-L-ornithine ((L)-NIO, 1 mg/kg/min for 5 min), the delayed hypotension was attenuated by a selective inducible NOS (iNOS) inhibitor, S-methylisothiourea (SMT, 0.5 mg/kg/min for 5 min). Administration of WSE also produced an elevation in plasma nitrate/nitrite concentration, as well as an increase in the expression of iNOS protein in the heart and thoracic aorta. These results indicate that WSE from the leaf of M. calabura elicited both a transient and delayed hypotensive effect via the production of NO. Furthermore, activation of NO/sGC/cGMP signaling pathway may mediate the M. calabura-induced hypotension.