Crystal structure of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1

Biphenyl dioxygenase is the enzyme that catalyzes the stereospecific dioxygenation of the aromatic ring. This enzyme has attracted the attention of researchers due to its ability to oxidize polychlorinated biphenyls, which is one of the serious environmental contaminants. We determined the crystal structure of the terminal oxygenase component of the biphenyl dioxygenase (BphA1A2) derived from Rhodococcus strain sp. RHA1 in substrate-free and complex forms. These crystal structures revealed that the substrate-binding pocket makes significant conformational changes upon substrate binding to accommodate the substrate into the pocket. Our analysis of the crystal structures suggested that the residues in the substrate-binding pocket can be classified into three groups, which, respectively, seem to be responsible for the catalytic reaction, the orientation/conformation of the substrate, and the conformational changes of the substrate-binding pocket. The cooperative actions of residues in the three groups seem to determine the substrate specificity of the enzyme.     

Mefenamic Acid Attenuates Chronic Alcohol Induced Cognitive Impairment in Zebrafish: Possible Role of Cholinergic Pathway

Based on the scientific evidence supporting the neuroinflammatory response contributes the cognitive impairment associated with chronic alcoholism and the neuroprotective actions of mefenamic acid with reversal of memory loss and brain inflammation in mice, this study was designed to evaluate the effect of mefenamic acid against chronic alcohol induced cognitive impairment in zebrafish model. Zebrafish were grouped and subjected to normal behavioral analysis in light–dark chamber for 10 days. The preference to dark compartment was noted in zebrafish. Zebrafish were grouped and exposed to escalating doses of alcohol for 28 days with and without mefenamic acid exposure (100 and 200 µg/L) and subjected to a fear conditioning passive avoidance task from day 13 of 28. The cognitive evaluation was performed for 10 days and the brain tissue was isolated to estimate acetylcholinesterase activity. In cognitive evaluation study, the normal zebrafish retained the memory of the learned task and avoided the dark. The alcohol exposed zebrafish showed impairment in retaining the memory of learned task. Mefenamic acid exposed zebrafish showed a significant protection against cognitive impairment caused by alcohol and retained the memory of learned task with a significant decrease in AChE activity in brain homogenate compared to alcohol exposed zebrafish. The results of this study suggest that the memory enhancing activity of mefenamic acid might be due to activation of cholinergic transmission that has protected neuroinflammatory and neurodegenerative conditions caused by alcohol.     

Pathogenic bacteria associated withLates calcarifer andAmbassis commersoni

Summary The estuarine fishesLates calcarifer andAmbassis commersoni are most commonly afflicted with fin rot and skin ulcer diseases, particularly during summer. Water and sediment samples, skin and gill of healthy fish, and skin, gill, liver, spleen, kidney and blood of diseased fish were screened for their quantitative and qualitative bacterial load. No direct relationship was found between the bacterial load of the environment and bacterial infection in fish.Micrococcus,Corynebacterium, Bacillus, Pseudomonas, Vibrio, Aeromonas andFlavobacterium-Cytophaga were encountered in both environmental samples and skin and gill of healthy fishes.Vibrio constituted the highest percentage in the skin and gill samples of diseased fishes, whilePseudomonas, Aeromonas andBacillus were observed only in smaller percentages.Vibrio alone was seen in the internal organs and blood of diseased fishes. Predominance ofVibrio over the other microflora, invasion of the fish tissues by theVibrio and the various factors which promote infection of fish by these pathogenic bacteria are discussed.

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Bactéries pathogènes associées avec Lates calcarifer et Ambassis commersoni

Résumé Les poissons d'estuaireLates calcarifer etAmbassis commersoni sont très fréquemment atteints de maladies de pourriture des nageoires et d'ulcères de la peau, particulièrement durant l'été. On a criblé l'eau, des échantillons de sédiments, la peau et les branchies de poissons sains, la peau, les branchies, le foie, la rate, le rein et le sang de poissons malades pour leur charge quantitative et qualitative en bactéries. On n'a trouvé aucune relation directe entre la charge bactérienne environnementale et l'infection bactérienne chez le poisson. On a trouvéMicrococcus, Corynebacterium, Bacillus, Pseudomonas, Vibrio, Aeromonas etFlavobacterium-Cytophaga tant dans les échantillons environnementaux que dans la peau et les branchies de poissons sains. LesVibrio constituaient le pourcentage le plus élevé de bactéries dans la peau et les branchies chez les poissons malades tandis que l'on observaitPseudomonas, Aeromonas, etBacillus en moindre pourcentage. On ne voyait que desVibrio dans les organes internes et le sang des poissons malades. On discute la prédominance deVibrio sur les autres microflores, l'invasion des tissus chez les poissons parVibrio et les différents facteurs qui favorisent l'infection chez les poissons par ces bactéries pathogènes.

     

Settlement and growth of the green mussel Perna viridis (L.) in coastal waters: influence of water velocity

Green mussels Perna viridis were observed to be a major foulant in the seawater intake tunnel of a coastal power station. Field experiments were carried out to ascertain what factors were responsible for the successful colonisation by mussels. Two adjacent stations (25 m apart) were selected, one representing the coastal waters and the other representing the intake screens (with higher water velocity). Gonadal activity, larval abundance, spat settlement and growth rate of the mussels were monitored at monthly intervals for a total period of two years. The results showed that the breeding activity of the mussels at the study area is influenced largely by temporal distribution of seawater temperature. However, ensuing larval availability in the coastal waters is more dependent on food availability. On the other hand, spat settlement and growth rate are predominantly influenced by water flow, probably as a result of increased propagule and food flux rate at higher water velocities. Higher water velocity at the intake screens also contributed to mussel dominance by preventing settlement of many potential competitors.     

Bacterial production of histamine in some tropical fish

Quantitative and qualitative distribution of histamine-forming bacteria associated with the fish Rastrelliger kanagurta, Sardinella longiceps, Sillago sihama and Liza subviridis, were investigated. These bacteria constituted a significant portion of the total bacterial population of fish and the values obtained in the present study were higher than those previously reported. The order of quantitative abundance of histamine-forming bacteria in the fish examined was: S. longiceps greater than R. kanagurta greater than S. sihama greater than L. subviridis. The bacterial genera isolated were Vibrio sp., Bacillus sp., Pseudomonas sp., Aeromonas sp. and Micrococcus sp., and among them Vibrio was dominant. Growth of the isolates (Vibrio sp., V. fischeri and Bacillus sp.) at different temperatures, pH and sodium chloride concentrations indicated them to be mesophilic, euryhaline and tolerant to acidic and alkaline pH. Bacillus sp. produced more histamine in R. kanagurta, while V. fisheri produced more histamine in S. longiceps.     

Effects of substrate binding on the dynamics of RNase A: Molecular dynamics simulations of UpA bound and native RNase A

RNase A has been extensively used as a model protein in several biophysical and biochemical studies. Using the available structural and biochemical results, RNase A-UpA interaction has been computationally modeled at an atomic level. In this study, the molecular dynamics (MD) simulations of native and UpA bound RNase A have been carried out. The gross dynamical behavior and atomic fluctuations of the free and UpA bound RNase A have been characterized. Principal component analysis is carried out to identify the important modes of collective motion and to analyze the changes brought out in these modes of RNase A upon UpA binding. The hydrogen bonds are monitored to study the atomic details of RNase A-UpA interactions and RNase A-water interactions. Based on these analysis, the stability of the free and UpA bound RNase A are discussed. © 1997 John Wiley & Sons, Inc. Biopoly 42: 505–520, 1997     

Inhibition of MG-63 cell proliferation and PDGF-stimulated cellular processes by inhibitors of phosphatidylinositol 3-kinase

Studies on a platelet-derived growth factor (PDGF) responsive osteosarcoma cell line, MG-63, were initiated to determine the effects of phosphatidylinositol (Ptdlns) 3-kinase inhibitors on serum-stimulated cell proliferation and PDGF-stimulated DNA replication, actin rearrangements, or Ptdlns 3-kinase activity. In a dose-dependent manner, the fungal metabolite wortmannin and a quercetin derivative, LY294002 (2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one), inhibited serum-stimulated MG-63 cell proliferation. The mitogenic effects of PDGF on MG-63 cells, as determined by incorporation of [³H]-thymidine, were also substantially inhibited in the presence of 0.10 μM wortmannin or 10 μM LY294002. Furthermore, MG-63 cells stimulated by PDGF form distinct actin-rich, finger-like membrane projections which are completely inhibited by either 0.10 μM wortmannin or 10 μM LY294002. At these same concentrations, wortmannin and LY294002 were also effective at reducing levels of phosphatidylinositol 3-phosphate in PDGF-stimulated MG-63 cells. Treatment of these cells with increasing concentrations of wortmannin reduced the level of PDGF stimulated tyrosine phosphorylation of the PDGF receptor but did not significantly affect the amount of the Ptdlns 3-kinase regulatory subunit, p85, associated with the receptor. Additionally, pretreatment of cells with 0.250 μM wortmannin followed by stimulation with PDGF resulted in a slightly reduced level of receptor autokinase activity; however, similar treatment with 50 μM LY294002 did not affect the level of autokinase activity. These results demonstrate the effects of two different Ptdlns 3-kinase inhibitors on serum- and PDGF-stimulated MG-63 cell proliferation and PDGF-stimulated morphological changes and suggest a greater role for Ptdlns 3-kinase in these processes. J. Cell. Biochem. 64:182–195. © 1997 Wiley-Liss, Inc.     

Planktonic Luminous Bacteria of Vellar Estuary,South India

Distribution of planktonic luminous bacteria in relation to environmental parameters was investigated at two stations located in the Vellar Estuary. Luminous microflora showed a pronounced seasonal cycle with very low counts during monsoon months followed by an increase in post monsoon and peak counts during summer. The population density of these procaryotes was remarkably high ranging from 3.5 to 33.1 colony forming units per ml. They constituted 2.1 to 52.1 % of the total bacterial counts. Salinity appeared to govern the distribution of luminous procaryotes as their counts corresponded well with fluctuations in salinity. Taxonomic affiliation of the isolates revealed predominance of Vibrio harveyi. Vibrio fischeri and Photobacterium leiognathi exhibited sparse distribution.