Molecular dynamics study of free energy profile for dissociation of ligand from CA I active site

We investigate the binding/dissociation process of ligand molecule from carbonicanhydrase (CA) I carbonic anhydrase (CA) I enzyme by using all-atom moleculardynamics simulation. The force field parameters of zinc ion in the CA I active site are estimatedby quantum chemical calculations and are summarized in this paper. The free energyprofile for binding/dissociation process of ligand from CA I active site is calculated by thethermodynamic integration combined with the all-atom molecular dynamics simulation. Thebinding free energy as a function of the distance between the center of mass positions of CAI active site and the ligand molecule is estimated. The radial distribution function of theCA I-ligand complex is calculated from the trajectory of all-atom molecular dynamics (MD)simulation. We estimate the free energy surface from the radial distribution function. Wecan obtain the bond constant of the equilibrium state from the value of the free energy surface.We discuss the binding/dissociation process of ligand molecule by calculating the freeenergy profile to know the stability of the CA I-ligand complex with some thermodynamicproperties such as the binding free energy, the equilibrium state of the free energy surfaceand so on

Changes in the expression of miRNAs at the pericentral and periportal regions of the rat liver in response to hepatocellular injury: comparison with the changes in the expression of plasma miRNAs

MicroRNAs (miRNAs) in body fluids have received attention as potential biomarkers of organ damage because miRNAs that are highly or specifically expressed in a given organ are likely released into body fluids as a result of damage to that organ. We previously determined that the plasma miRNA profile in rats was dramatically changed due to acetaminophen (APAP)-induced pericentral necrosis and methapyrilene (MP)-induced periportal necrosis in the liver. The purpose of this study was to examine whether the expression of hepatic miRNAs is differentially modulated at different zones due to injury and to examine the relationship of the hepatic miRNA profile with the changes in the plasma miRNA expression profile. Through the laser microdissection of the periportal and periportal regions of the liver and TaqMan microRNA Array analysis, we found that 49 miRNAs are differentially expressed between the pericentral and periportal regions of control rats. In both APAP- and MP-treated rats, the miRNAs that presented decreased expression dominated in both the injured and non-injured areas compared with the miRNAs that exhibited increased expression. The changes in miRNA expression in each region of the liver were compared with those observed in the plasma. Of the 301 plasma miRNAs with expression that was changed as a result of APAP administration, only 21% were changed in the injured area of the liver. Of the 263 plasma miRNAs with expression that was changed due to MP administration, only 24% were changed in the injured area of the liver. Thus, the miRNA expression profiles in the plasma do not merely reflect the release of miRNAs from the damaged cells in the liver. This report provides the first demonstration of zonal miRNA expression in the liver and of the relationship of the miRNA expression profile in a tissue with the plasma miRNA profile. © 2014 Elsevier Ireland Ltd

A Novel Mouse Model for Phenytoin-Induced Liver Injury: Involvement of Immune-Related Factors and P450-Mediated Metabolism

Drug-induced liver injury is an important issue for drug development and clinical drug therapy; however, in most cases, it is difficult to predict or prevent these reactions due to a lack of suitable animal models and the unknown mechanisms of action. Phenytoin (DPH) is an anticonvulsant drug that is widely used for the treatment of epilepsy. Some patients who are administered DPH will suffer symptoms of drug-induced liver injury characterized by hepatic necrosis. DPH-induced liver injury occurs in 1 in 1000 or 1 in 10 000 patients. Clinically, 75% of patients who develop liver injury develop a fever and 63% develop a rash. In this study, we established a mouse model for DPH-induced liver injury and analyzed the mechanisms for hepatotoxicity in the presence of immune-related or inflammation-related factors and metabolic activation. Female C57BL/6 mice were administered DPH for 5 days in combination with l-buthionine-S,R-sulfoximine. Then, the plasma alanine aminotransferase (ALT) levels were increased, hepatic lesions were observed during the histological evaluations, the hepatic glutathione levels were significantly reduced, and the oxidative stress marker levels were significantly increased. The inhibition of cytochrome P450-dependent oxidative metabolism significantly suppressed the elevated plasma ALT levels and depleted hepatic glutathione. Among the innate immune factors, the hepatic mRNA levels of NACHT, LRR, pyrin domain-containing protein 3, interleukin-1β, and damage-associated molecular patterns were significantly increased. Prostaglandin E 1 treatment ameliorated the hepatic injury caused by DPH. In conclusion, cytochrome P450-dependent metabolic activation followed by the stimulation of the innate immune responses is involved in DPHinduced liver injury

Retinoid X receptor α in human liver is regulated by miR-34a

Retinoid X receptor α (RXRα) forms a heterodimer with numerous nuclear receptors to regulate drug- or lipid-metabolizing enzymes. In this study, we investigated whether human RXRα is regulated by microRNAs. Two potential recognition elements of miR-34a were identified in the RXRα mRNA: one in the coding region and the other in the 3′-untranslated region (3′-UTR). Luciferase assays revealed that miR-34a recognizes the element in the coding region. The overexpression of miR-34a in HepG2 cells significantly decreased the endogenous RXRα protein and mRNA levels. The stability of RXRα mRNA was decreased by the overexpression of miR-34a, indicating that miR-34a negatively regulates RXRα expression by facilitating mRNA degradation. We found that the miR-34a-dependent down-regulation of RXRα decreases the induction of CYP26 and the transactivity of CYP3A4. miR-34a has been reported to be up-regulated by p53, which has an ability to promote liver fibrosis. The p53 activation resulted in an increase of the miR-34a level and a decrease of the RXRα protein level. In addition, the miR-34a levels in eight fibrotic livers were higher than those in six normal livers, and the reverse trend was found for the RXRα protein levels. An inverse correlation was observed between the miR-34a and the RXRα protein levels in the 14 samples. Taken together, the data show that miR-34a negatively regulates RXRα expression in human liver, and affects the expression of its downstream genes. This miR-34a-dependent regulation might be the underlying mechanism responsible for the decreased expression of the RXRα protein in fibrotic livers. © 2014 Elsevier Inc

Long-term monitoring of the short period SU UMa-type dwarf nova, V844 Herculis

We report on time-resolved CCD photometry of four outbursts of a short-period SU UMa-type dwarf nova, V844 Herculis. We successfully determined the mean superhump periods to be 0.05584(64) days, and 0.055883(3) for the 2002 May superoutburst, and the 2006 April-May superoutburst, respectively. During the 2002 October observations, we confirmed that the outburst is a normal outburst, which is the first recorded normal outburst in V844 Her. We also examined superhump period changes during 2002 May and 2006 April-May superoutbursts, both of which showed increasing superhump period over the course of the plateau stage. In order to examine the long-term behavior of V844 Her, we analyzed archival data over the past ten years since the discovery of this binary. Although photometry is not satisfactory in some superoutbursts, we found that V844 Her showed no precursors and rebrightenings. Based on the long-term light curve, we further confirmed V844 Her has shown almost no normal outbursts despite the fact that the supercycle of the system is estimated to be about 300 days. In order to explain the long-term light curves of V844 Her, evaporation in the accretion disk may play a role in the avoidance of several normal outbursts, which does not contradict with the relatively large X-ray luminosity of V844 Her.Comment: 10 pages, 11 figures, accepted for PAS

Plasma MicroRNA Profiles in Rat Models of Hepatocellular Injury, Cholestasis, and Steatosis

MicroRNAs (miRNAs) are small RNA molecules that function to modulate the expression of target genes, playing important roles in a wide range of physiological and pathological processes. The miRNAs in body fluids have received considerable attention as potential biomarkers of various diseases. In this study, we compared the changes of the plasma miRNA expressions by acute liver injury (hepatocellular injury or cholestasis) and chronic liver injury (steatosis, steatohepatitis and fibrosis) using rat models made by the administration of chemicals or special diets. Using miRNA array analysis, we found that the levels of a large number of miRNAs (121–317 miRNAs) were increased over 2-fold and the levels of a small number of miRNAs (6–35 miRNAs) were decreased below 0.5-fold in all models except in a model of cholestasis caused by bile duct ligation. Interestingly, the expression profiles were different between the models, and the hierarchical clustering analysis discriminated between the acute and chronic liver injuries. In addition, miRNAs whose expressions were typically changed in each type of liver injury could be specified. It is notable that, in acute liver injury models, the plasma level of miR-122, the most abundant miRNA in the liver, was more quickly and dramatically increased than the plasma aminotransferase level, reflecting the extent of hepatocellular injury. This study demonstrated that the plasma miRNA profiles could reflect the types of liver injury (e.g. acute/chronic liver injury or hepatocellular injury/cholestasis/steatosis/steatohepatitis/fibrosis) and identified the miRNAs that could be specific and sensitive biomarkers of liver injury

Practical Science and Environmental Education Workshop in Manaus, Brazil

It is an unequivocal fact that Amazonian tropical forest is the largest remaining primary forest in the world. The ecosystem in the region is e tremely comple with high biodiversity (Peres et al. 2010). Conservation and protection of the dynamic forest and river regions is e tremely important not only for the natural environments, but also for the economy and social dependence of benefits from such abundant natural environments. Important natural parameters that affect status of the natural environments include light (natural sunlight), soil, and water, which abundantly e ist in the Amazon region. Solar energy is the primary energy source for the majority of living organisms in both terrestrial and aquatic ecosystems, and drives the diurnal and seasonal cycles of biogeochemical processes (Monteith & Unsworth 2013). In particular, in situ light data remains one of the most underappreciated data measurements although having a significant impact on the physical, chemical and biological processes in the ecosystem (Johnsen 2012). Soil provides the fundamental basis for all terrestrial living organisms including the Amazonian forests as well as life-sustaining infrastructure for human society. Water is the most essential single entity to constitute all organisms from a single cell to the earth. Understanding of importance and roles of each factor and interaction of such comple dynamics in the natural environments can serve as fundamental platform for natural scientists, particularly for young scientists such as university students. The objective of this workshop was to provide hand- on scientific and environmental education for university students in Manaus, Amazonas, Brazil through practical field measurements using the three most important parameters in the natural ecosystem composed of natural sunlight, soil, and water. The workshop was divided into a series of lectures, in situ field sampling, and data processing, analysis and interpretation with the ultimate goal of empowering the undergraduate students with research-centered environmental education and e perience of developing international collaboration.departmental bulletin pape