Scipion web tools: Easy to use cryo-EM image processing over the web

Mon, 01 Jan 2018 00:00:00 GMT

Scipion web tools: Easy to use cryo-EM image processing over the web Conesa Mingo, P; Gutierrez, J; Quintana, A; de la Rosa Trevin, JM; Zaldivar-Peraza, A; Cuenca Alba, J; Kazemi, M; Vargas, J; del Cano, L; Segura, J; Sorzano, COS; Maria Carazo, J Macromolecular structural determination by Electron Microscopy under cryogenic conditions is revolutionizing the field of structural biology, interesting a large community of potential users. Still, the path from raw images to density maps is complex, and sophisticated image processing suites are required in this process, often demanding the installation and understanding of different software packages. Here, we present Scipion Web Tools, a web-based set of tools/workflows derived from the Scipion image processing framework, specially tailored to nonexpert users in need of very precise answers at several key stages of the structural elucidation process.

Aligning pedagogy and space: An Australian evidence-based approach

Mon, 01 Jan 2018 00:00:00 GMT

Aligning pedagogy and space: An Australian evidence-based approach Imms, W

Improving Assimilation of Radiance Observations by Implementing Model Space Localization in an Ensemble Kalman Filter

Sat, 01 Dec 2018 00:00:00 GMT

Improving Assimilation of Radiance Observations by Implementing Model Space Localization in an Ensemble Kalman Filter Lei, L; Whitaker, JS; Bishop, C

Therapeutic potential of targeting the protective arm of the renin angiotensin system in cirrhotic and non-cirrhotic portal hypertension

Tue, 01 Jan 2019 00:00:00 GMT

Therapeutic potential of targeting the protective arm of the renin angiotensin system in cirrhotic and non-cirrhotic portal hypertension Gunarathne, Withanage Don Lakmie Suranjika Portal hypertension (PHT) and bleeding from gastroesophageal varices is the major cause of morbidity and mortality in cirrhotic patients. In cirrhotics, splanchnic vasodilatation leading to an elevated portal venous inflow plays an important role in the pathogenesis of PHT. Although the current pharmacological mainstay to reduce portal pressure by decreasing splanchnic inflow is non-selective beta-blockade, most patients (>60%) do not achieve an optimal response and 15% of patients are unable to tolerate these drugs. The peptide angiotensin-(1-7) (Ang-(1-7)) and Mas receptor (MasR) of the so called alternate axis of the renin angiotensin system (RAS) contributes to the pathological splanchnic vasodilatation in cirrhosis. Recent findings suggest that the vasodilatory effects of Ang-(1-7) could also be mediated via the Mas related G-protein coupled receptor type D (MrgD), a newly identified receptor of the alternate RAS. However, the effects of this receptor in mediating splanchnic vasodilatation are largely unknown. The experiments in this thesis aimed to investigate the effects of the blockade of the vasodilatory receptor MrgD in reducing portal pressure, and to compare them with those of MasR blockade, in cirrhotic and non-cirrhotic portal hypertensive rats. For the experiments in cirrhotic rats, the bile duct ligated (BDL) and carbon tetrachloride injected (CCl4) rat models were used. To investigate the short-term (acute treatment) effects of receptor blocker treatment, the MrgD blocker D-Pro7-Ang-(1-7) (D-Pro) (10µg/kg) or MasR blocker A779 (10µg/kg) were administered as an intravenous bolus injection. To study the long-term treatment (chronic treatment) effects, the BDL and CCl4 rats received a continuous infusion of either A779 or D-Pro at 28µg/kg/hr for 2 weeks, via subcutaneously implanted osmotic mini-pumps. Following the treatment, the rats were used for the measurement of portal pressure and mean arterial pressure (MAP). In these experiments, microsphere injections were performed to measure vascular resistance and regional blood flow. Mesenteric resistance vessels obtained from a separate group of CCl4 rats receiving long-term receptor blocker treatments or vessels isolated from saline-infused diseased rats and subjected to in-vitro blocker treatments, were used in a vessel myograph, to study the vasodilatory response to acetylcholine (Ach). In addition, we have also studied the potential use of a combination therapy of MrgD and MasR blockers in counteracting systemic hypotensive effects of the AT1R blocker losartan, because AT1R blockers are drugs that potentially can be used as anti-fibrotic and portal pressure lowering agents in fibrotic livers. To investigate the effects of short-term (acute treatment) combination therapy, D-Pro or A779 were injected 20 minutes after a bolus injection of losartan. To study the effects of long-term (chronic treatment) combination therapy, cirrhotic BDL rats received a long-term infusion of A779 or D-Pro via osmotic mini-pumps, combined with daily oral gavage injection of losartan for the same duration i.e. 2 weeks, prior to use in pressure measurement and/or regional blood flow studies. The effects of the short-term and long-term treatment of MrgD or MasR blockers on portal pressure and regional blood flows were also studied in the non-cirrhotic rat model of partial portal vein ligation (PPVL). In addition, the contribution of RAS to the development of PHT in the non-cirrhotic PPVL rat model was also studied using a time-course experiment. In these studies, changes in portal pressure at each time point were compared to the RAS gene expression profiles in the mesenteric vessels. Short-term therapy of both MrgD and MasR blockers significantly (p<0.001) reduced portal pressure in the cirrhotic BDL and CCl4 rats. However, a long-term continuous infusion of these blockers produced remarkable effects in cirrhotic portal hypertensive rats. The long-term treatment with D-Pro produced more profound inhibitory effect on portal pressure compared to that of A779. This prominent effect of D-Pro on portal pressure was likely related to its potent effect in inhibiting splanchnic vasodilatation which resulted in markedly increased splanchnic vascular resistance (SPVR), leading to a marked reduction in mesenteric blood flow (MBF). In keeping with these findings, vascular myograph experiments suggested that treatment with D-Pro but not A779, specifically inhibited the vasodilatory responses of 1st order as well as 2nd/3rd order mesenteric vessels to Ach, thus suggesting splanchnic vasculature-specific effects of MrgD in cirrhotic rats. Moreover, MasR but not MrgD blockade produced off target effects in the renal and hepatic vascular beds, confirming that unlike the MasR, MrgD plays a splanchnic vasculature-specific role in cirrhosis. A bolus injection of AT1R blocker losartan also reduced portal pressure in cirrhotic rats. However, despite its anti-fibrotic effects with improved intrahepatic vascular tone, long-term treatment with losartan failed to reduce portal pressure, likely due to its potent effects in reducing systemic and splanchnic vascular resistance and thereby increasing mesenteric blood flow coupled with increased cardiac output. Moreover, the systemic hypotensive effect produced by losartan could not be counteracted with a short-term or long-term combination therapy with D-Pro or A779. On the other hand, neither the MrgD nor MasR blockade were able to alter splanchnic vascular resistance or mesenteric blood flow in non-cirrhotic PPVL rats, which was supported by unaltered gene expression of both these receptors in the mesenteric vessels of PPVL rats compared to healthy controls. However, it appears that in PPVL rats, downregulation of vasoconstrictive classical RAS and in particular, AT1R expression in the mesenteric vessels contributed to splanchnic vasodilatation. In conclusion, blockade of the vasodilatory receptors of the alternate RAS; the MasR (22%) and in particular, the MrgD (33%), produces a clinically significant reduction of portal pressure (>20% from baseline) in cirrhotic rats. We also conclude that the effects of MrgD blockade but not MasR blockade, are splanchnic vasculature-specific and therefore, this newly characterized receptor, MrgD, is an ideal target to develop future therapeutics to treat PHT in cirrhosis. Based on findings from non-cirrhotic PPVL model, we conclude that the alternate RAS does not contribute to PHT in the absence of cirrhosis. Furthermore, a reduced activity of the classic RAS with specific reference to AT1R in the mesenteric vasculature appears to be play a role in pathological vasodilatation in non-cirrhotic PHT. © 2019 Dr. Withanage Don Lakmie Suranjika Gunarathne

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Scipion web tools: Easy to use cryo-EM image processing over the web

Aligning pedagogy and space: An Australian evidence-based approach

Improving Assimilation of Radiance Observations by Implementing Model Space Localization in an Ensemble Kalman Filter

Therapeutic potential of targeting the protective arm of the renin angiotensin system in cirrhotic and non-cirrhotic portal hypertension