T. F. Lowry

Production of 20-HETE and Its Role in Autoregulation of Cerebral Blood Flow

In the brain, pressure-induced myogenic constriction of cerebral arteriolar muscle contributes to autoregulation of cerebral blood flow (CBF). This study examined the role of 20-HETE in autoregulation of CBF in anesthetized rats. The expression of P-450 4A protein and mRNA was localized in isolated cerebral arteriolar muscle of rat by immunocytochemistry and in situ hybridization. The results of reverse transcriptase-polymerase chain reaction studies revealed that rat cerebral microvessels express cytochrome P-450 4A1, 4A2, 4A3, and 4A8 isoforms, some of which catalyze the formation of 20-HETE from arachidonic acid. Cerebral arterial microsomes incubated with [(14)C]arachidonic acid produced 20-HETE. An elevation in transmural pressure from 20 to 140 mm Hg increased 20-HETE concentration by 6-fold in cerebral arteries as measured by gas chromatography/mass spectrometry. In vivo, inhibition of vascular 20-HETE formation with N-methylsulfonyl-12, 12-dibromododec-11-enamide (DDMS), or its vasoconstrictor actions using 15-HETE or 20-hydroxyeicosa-6(Z),15(Z)-dienoic acid (20-HEDE), attenuated autoregulation of CBF to elevations of arterial pressure. In vitro application of DDMS, 15-HETE, or 20-HEDE eliminated pressure-induced constriction of rat middle cerebral arteries, and 20-HEDE and 15-HETE blocked the vasoconstriction action of 20-HETE. Taken together, these data suggest an important role for 20-HETE in the autoregulation of CBF.

The Rat Genome Database 2009: variation, ontologies and pathways

The Rat Genome Database (RGD, http://rgd.mcw.edu) was developed to provide a core resource for rat researchers combining genetic, genomic, pathway, phenotype and strain information with a focus on disease. RGD users are provided with access to structured and curated data from the molecular level through to the level of the whole organism, including the variations associated with disease phenotypes. To fully support use of the rat as a translational model for biological systems and human disease, RGD continues to curate these datasets while enhancing and developing tools to allow efficient and effective access to the data in a variety of formats including linear genome viewers, pathway diagrams and biological ontologies. To support pathophysiological analysis of data, RGD Disease Portals provide an entryway to integrated gene, QTL and strain data specific to a particular disease. In addition to tool and content development and maintenance, RGD promotes rat research and provides user education by creating and disseminating tutorials on the curated datasets, submission processes, and tools available at RGD. By curating, storing, integrating, visualizing and promoting rat data, RGD ensures that the investment made into rat genomics and genetics can be leveraged by all interested investigators.

The Rat Genome Database 2013—data, tools and users

The Rat Genome Database (RGD) was started >10 years ago to provide a core genomic resource for rat researchers. Currently, RGD combines genetic, genomic, pathway, phenotype and strain information with a focus on disease. RGD users are provided with access to structured and curated data from the molecular level through the organismal level. Those users access RGD from all over the world. End users are not only rat researchers but also researchers working with mouse and human data. Translational research is supported by RGD’s comparative genetics/genomics data in disease portals, in GBrowse, in VCMap and on gene report pages. The impact of RGD also goes beyond the traditional biomedical researcher, as the influence of RGD reaches bioinformaticians, tool developers and curators. Import of RGD data into other publicly available databases expands the influence of RGD to a larger set of end users than those who avail themselves of the RGD website. The value of RGD continues to grow as more types of data and more tools are added, while reaching more types of end users.

Postnatal changes in ventilation during normoxia and acute hypoxia in the rat: implication for a sensitive period.

Previously, we found heightened expression of inhibitory neurochemicals and depressed expression of excitatory neurochemicals with a sudden drop in metabolic activity around postnatal day (P) 12 in rat brainstem respiratory nuclei, suggesting that this period is a critical window during which respiratory control or regulation may be distinctly different. To test this hypothesis, the hypoxic ventilatory responses (HVR) to 10% oxygen were tested in rats every day from P0 to P21. Our data indicate that (1) during normoxia (N), breathing frequency (f) increased with age, peaking at P13, followed by a gradual decline, whereas both tidal volume (VT) and minute ventilation () significantly increased in the second postnatal week, followed by a progressive increase in VT and a relative plateau in ; (2) during 5 min of hypoxia (H), exhibited a biphasic response from P3 onward. Significantly, the ratio of to was generally > 1 during development, except for P13–16, when it was < 1 after the first 1–2 min, with the lowest value at P13; (3) the H : N ratio for f, VT and during the first 30 s and the last minute of hypoxia all showed a distinct dip at P13, after which the VT and values rose again, while the f values declined through P21; and (4) the H : N ratios for f, VT and averaged over 5 min of hypoxia all exhibited a sudden fall at P13. The f ratio remained low thereafter, while those for VT and increased again with age until P21. Thus, hypoxic ventilatory response is influenced by both f and VT before P13, but predominantly by VT after P13. The striking changes in normoxic ventilation as well as HVR at or around P13, together with our previous neurochemical and metabolic data, strongly suggests that the end of the second postnatal week is a critical period of development for brainstem respiratory nuclei in the rat.

Important role of carotid chemoreceptor afferents in control of breathing of adult and neonatal mammals

This review provides a summary and prospective on the importance of carotid/peripheral chemoreceptors to the control of breathing during physiologic conditions. For several days after carotid body denervation (CBD), adult mammals hypoventilate (+10 mmHg increase in Pa(CO(2))) at rest and during exercise and CO(2) sensitivity is attenuated by about 60%. In addition, if the rostral ventrolateral medulla is cooled during NREM sleep after CBD, a sustained apnea is observed. Eventually, days or weeks after CBD, a peripheral ventilatory chemoreflex redevelops and there is a normalization of breathing (rest and exercise) and CO(2) sensitivity. The site (s) of the regained chemosensitivity has not been established. This plasticity/redundancy after CBD appears greater in neonates than in adult mammals. These data suggest the carotid and other peripheral chemoreceptors provide an important excitatory input to medullary respiratory neurons that is essential for breathing when wakeful stimuli and central chemoreceptors are absent.

Effect on breathing of surface ventrolateral medullary cooling in awake, anesthetized and asleep goats

In adult and neonatal goats, we chronically implanted thermodes on the ventrolateral (VLM) medullary surface to create reversible neuronal dysfunction and thereby gain insight into the role of superficial VLM neurons in control of breathing in anesthetized, awake and asleep states. Consistent with data of others, cooling caudal area M and rostral area S caused sustained apnea under anesthesia. However, in the awake and NREM sleep states, cooling at this site caused only a modest reduction in breathing, indicating that neurons at this site are not critical for respiratory rhythm in these states. Moreover, data in the awake state over multiple conditions suggest neurons at this site do not integrate all intracranial and carotid chemoreception. The data suggest though that neurons at this site have a facilitatory-like effect on breathing both unrelated and related to intracranial chemoreception. We believe that this facilitation serves a function similar to the facilitation provided by the carotid chemoreceptors and by sources associated with wakefulness. Accordingly, elimination/attenuation of any one of these three influences (caudal M rostral S VLM, wakefulness, carotid chemoreception) results in a slight decrease in breathing, removal of two of the three results in a greater decrease in breathing, and removal of all three results in sustained apnea.

Structural and functional alterations in the rat lung following whole thoracic irradiation with moderate doses: injury and recovery

Purpose: To characterize structural and functional injuries following a single dose of whole-thorax irradiation that might be survivable after a nuclear attack/accident. Methods: Rats were exposed to 5 or 10 Gy of X-rays to the whole thorax with other organs shielded. Non-invasive measurements of breathing rate and arterial oxygen saturation, and invasive evaluations of bronchoalveolar lavage fluid, (for total protein, Clara cell secretory protein), vascular reactivity and histology were conducted for at least 6 time points up to 52 weeks after irradiation. Results: Irradiation with 10 Gy resulted in increased breathing rate, a reduction in oxygen saturation, an increase in bronchoalveolar lavage fluid protein and attenuation of vascular reactivity between 4–12 weeks after irradiation. These changes were not observed with the lower dose of 5 Gy. Histological examination revealed perivascular edema at 4–8 weeks after exposure to both doses, and mild fibrosis beyond 20 weeks after 10 Gy. Conclusions: Single-dose exposure of rat thorax to 10 but not 5 Gy X-irradiation resulted in a decrease in oxygen uptake and vasoreactivity and an increase in respiratory rate, which paralleled early pulmonary vascular pathology. Vascular edema resolved and was replaced by mild fibrosis beyond 20 weeks after exposure, while lung function recovered.

Postnatal development of metabolic rate during normoxia and acute hypoxia in rats: implication for a sensitive period

Previously, we reported that the hypoxic ventilatory response (HVR) in rats was weakest at postnatal day (P) P13, concomitant with neurochemical changes in respiratory nuclei. A major determinant of minute ventilation (Ve) is reportedly the metabolic rate [O(2) consumption (Vo(2)) and CO(2) production (Vco(2))]. The present study aimed at testing our hypothesis that daily metabolic rates changed in parallel with ventilation during development and that a weak HVR at P13 was attributable mainly to an inadequate metabolic rate in hypoxia. Ventilation and metabolic rates were monitored daily in P0-P21 rats. We found that 1) ventilation and metabolic rates were not always correlated, and Ve/Vo(2) and Ve/Vco(2) ratios were not constant during development; 2) metabolic rate and Ve/Vo(2) and Ve/Vco(2) ratios at P0-P1 were significantly different from the remaining first postnatal week in normoxia and hypoxia; 3) at P13, metabolic rates and Ve/Vo(2) and Ve/Vco(2) ratios abruptly increased in normoxia and were compromised in acute hypoxia, unlike more stable trends during the remaining second and third postnatal weeks; and 4) the respiratory quotient (Vco(2)/Vo(2)) was quite stable in normoxia and fluctuated slightly in hypoxia from P0 to P21. Thus our data revealed heretofore unsuspected metabolic adjustments at P0-P1 and P13. At P0-P1, ventilation and metabolic rates were uncorrelated, whereas at P13, they were closely correlated under normoxia and hypoxia. The findings further strengthened the existence of a critical period of respiratory development around P13, when multiple physiological and neurochemical adjustments occur simultaneously.

The pathway ontology - updates and applications

BackgroundThe Pathway Ontology (PW) developed at the Rat Genome Database (RGD), covers all types of biological pathways, including altered and disease pathways and captures the relationships between them within the hierarchical structure of a directed acyclic graph. The ontology allows for the standardized annotation of rat, and of human and mouse genes to pathway terms. It also constitutes a vehicle for easy navigation between gene and ontology report pages, between reports and interactive pathway diagrams, between pathways directly connected within a diagram and between those that are globally related in pathway suites and suite networks. Surveys of the literature and the development of the Pathway and Disease Portals are important sources for the ongoing development of the ontology. User requests and mapping of pathways in other databases to terms in the ontology further contribute to increasing its content. Recently built automated pipelines use the mapped terms to make available the annotations generated by other groups.ResultsThe two released pipelines – the Pathway Interaction Database (PID) Annotation Import Pipeline and the Kyoto Encyclopedia of Genes and Genomes (KEGG) Annotation Import Pipeline, make available over 7,400 and 31,000 pathway gene annotations, respectively. Building the PID pipeline lead to the addition of new terms within the signaling node, also augmented by the release of the RGD “Immune and Inflammatory Disease Portal” at that time. Building the KEGG pipeline lead to a substantial increase in the number of disease pathway terms, such as those within the ‘infectious disease pathway’ parent term category. The ‘drug pathway’ node has also seen increases in the number of terms as well as a restructuring of the node. Literature surveys, disease portal deployments and user requests have contributed and continue to contribute additional new terms across the ontology. Since first presented, the content of PW has increased by over 75%.ConclusionsOngoing development of the Pathway Ontology and the implementation of pipelines promote an enriched provision of pathway data. The ontology is freely available for download and use from the RGD ftp site at ftp://rgd.mcw.edu/pub/ontology/pathway/ or from the National Center for Biomedical Ontology (NCBO) BioPortal website at http://bioportal.bioontology.org/ontologies/PW.

The Rat Genome Database Curators: Who, What, Where, Why

abstracts. As can be seen by the amount oftime spent in curation, the time savings forresearchers are substantial. Education and Outreach An essential part of the curator’s job is toprovide education and training for RGDusers and potential users. This is accom-plished in several ways. The RGD Web sitecontains a ‘‘Help’’ section developed by thecurators and which is accessible from allpages. This component contains a Glossaryof Terms, general information on how touse the searches and tools, a FrequentlyAsked Questions (FAQ) section, and acomponent that walks users through typicaluse case scenarios. Curators also handleindividual questions through the userrequest system accessible via the ContactUs button on each page, and throughtelephone calls and the Rat CommunityForum. RGD has published seven tutorialvideos at SciVee (http://www.scivee.tv/), aWeb site for video publications for re-search, and videos are available at RGD aswell. Curators present tutorials at majorconferences such as Experimental Biology,Society of Toxicology, Neuroscience andRat Genomics and Models, as well asindividual rat research laboratories. Inaddition, RGD is well represented at majorconferences such as Biology of Genomes,Genome Informatics, Intelligent Systemsfor Molecular Biology, and the Interna-tional Mammalian Genome Conferencewith presentations and posters highlightingnew tools and datasets. Other outreachactivities involve contact with individualresearchers for nomenclature assignment togenes, QTLs, and strains, as well asconstruction of customized datasets.