Anaerobic degradation of papermill sludge in a two-phase digester containing rumen microorganisms and colonized polyurethane foam

Summary The use of reticulated polyurethane foam as a support material for the immobilization of methanogenic associations and its application to the anaerobic treatment of fine particulate solid wastes was investigated. The colonization of polyurethane support particles in a continuous upflow reactor fed on a mixture of acetate, propionate and butyrate, was both rapid and dense. The combination of rumen microorganisms and colonized support particles in a two-phase digester resulted in an efficient anaerobic decomposition of papermill sludge.     

On the validity of the genusDactylococcopsis (Cyanophyceae)

Summary The genusDactylococcopsis Hansg. 1888 (Cyanophyceae) is based on the typeD. rupestris, which was later identified as a green algae. Most of the many species described later were also placed to other groups of algae. Several authors even doubted about the existence of the genus. As, however, some species of Cyanophyceae correspond to the original generic diagnosis, the name Dactylococcopsis Hansg. ex R. et F.Chod. 1925 has been proposed as a nomen conservandum, and a new type (D. smithii R. et F.Chod.) has been defined. Further speciesD. linearis Geitl. 1935 and D.Planctonica Teil. 1942 has been unambiguously described till now.     

The mechanism of high affinity pentasaccharide binding to antithrombin,insights from Gaussian accelerated molecular dynamics simulations

Abstract

The activity of antithrombin (AT), a serpin protease inhibitor, is enhanced by heparin and heparin analogs against its target proteases, mainly thrombin, factors Xa and IXa. Considerable amount of information is available on the multistep mechanism of the heparin pentasaccharide binding and conformational activation. However, much of the details were inferred from ‘static’ structures obtained by X-ray diffraction. Moreover, limited information is available for the early steps of binding mechanism other than kinetic studies with various ligands. To gain insights into these processes, we performed enhanced sampling molecular dynamics (MD) simulations using the Gaussian Accelerated Molecular Dynamics (GAMD) method, applied previously in drug binding studies. We were able to observe the binding of the pentasaccharide idraparinux to a ‘non-activated’ AT conformation in two separate trajectories with low root mean square deviation (RMSD) values compared to X-ray structures of the bound state. These trajectories along with further simulations of the AT-pentasaccharide complex provided insights into the mechanisms of multiple conformational transitions, including the expulsion of the hinge region, the extension of helix D and the conformational behavior of the reactive center loop (RCL). We could also confirm the high stability of helix P in non-activated AT conformations, such states might play an important role in heparin binding. ‘Generalized correlation’ matrices revealed possible paths of allosteric signal propagation to the binding sites for the target proteases, factors Xa and IXa. Enhanced MD simulations of ligand binding to AT may assist the design of new anticoagulant drugs.

Communicated by Ramaswamy H. Sarma     

A curious occurrence of Hazenia broadyi spec. nova in Antarctica and the review of the genus Hazenia (Ulotrichales, Chlorophyceae)

Freshwater filamentous green algae with branched thalli are almost unknown from the Antarctic region. They have rarely been recorded from maritime Antarctica and from sub-Antarctic Islands with rich phanerogamic vegetation. In the genus Hazenia, only one unidentified species was reported from several subaerial sites on Signy Island in 1979. However, unique populations of this genus were recently found in the stony littoral zone of two stable shallow lakes in the northern deglaciated region of James Ross Island (NE Antarctic Peninsula). These populations have a specialized ecology; they participate in the microvegetation on the flattened surfaces of stones in the littoral zones of lakes. The dominant green filamentous and richly branched alga from these communities was transferred to monospecific culture and studied in detail. Molecular sequence data (18S ribosomal DNA and the internal transcribed spacer) indicate that it belongs to the genus Hazenia (Bold in Am J Bot 45:737–743, 1958). Based on distinct molecular, morphological, and ecological characters, this alga was described as a new species (Hazenia broadyi spec. nova). A review of the genus Hazenia, based on molecular phylogenetic analyses of available strains, was also performed.