Study on the hydrolysis mechanism of phosphodiesterase 4 using molecular dynamics simulations

We carried out NPT molecular dynamics simulations in an explicit solvent to better understand the mechanism of cyclic adenosine monophosphates (cAMP) hydrolysis by phosphodiesterase 4 (PDE4) enzyme on atomic details and to obtain information on the dynamics characteristic of the catalytic domains of PDE4. In analyzing the water hydrogen-bond network around the active site, we also showed the importance of water in drug–protein interactions. In addition, we reported the characteristics of the hydration pattern and the dynamic distance distribution around the interesting residues. The results indicated that Asp318 plays the role of a general base that can activate water molecule for nucleophilic attack on cAMP. As expected, His160 plays the role of a proton donor for cAMP.     

Inferred L/M cone opsin polymorphism of ancestral tarsiers sheds dim light on the origin of anthropoid primates

Tarsiers are small nocturnal primates with a long history of fuelling debate on the origin and evolution of anthropoid primates. Recently, the discovery of M and L opsin genes in two sister species, Tarsius bancanus (Bornean tarsier) and Tarsius syrichta (Philippine tarsier), respectively, was interpreted as evidence of an ancestral long-to-middle (L/M) opsin polymorphism, which, in turn, suggested a diurnal or cathemeral (arrhythmic) activity pattern. This view is compatible with the hypothesis that stem tarsiers were diurnal; however, a reversion to nocturnality during the Middle Eocene, as evidenced by hyper-enlarged orbits, predates the divergence of T. bancanus and T. syrichta in the Late Miocene. Taken together, these findings suggest that some nocturnal tarsiers possessed high-acuity trichromatic vision, a concept that challenges prevailing views on the adaptive origins of the anthropoid visual system. It is, therefore, important to explore the plausibility and antiquity of trichromatic vision in the genus Tarsius. Here, we show that Sulawesi tarsiers (Tarsius tarsier), a phylogenetic out-group of Philippine and Bornean tarsiers, have an L opsin gene that is more similar to the L opsin gene of T. syrichta than to the M opsin gene of T. bancanus in non-synonymous nucleotide sequence. This result suggests that an L/M opsin polymorphism is the ancestral character state of crown tarsiers and raises the possibility that many hallmarks of the anthropoid visual system evolved under dim (mesopic) light conditions. This interpretation challenges the persistent nocturnal–diurnal dichotomy that has long informed debate on the origin of anthropoid primates.     

The elevational gradient of Andean plant endemism: varying influences of taxon-specific traits and topography at different taxonomic levels

Aim Little is known about the elevational gradient of plant endemism. It is mostly assumed that patterns are determined by topographical factors such as area of elevational belts and degree of habitat fragmentation, but comparative studies of different plant taxa along the same elevational gradient are lacking. The aim was to compare the elevational patterns of plant endemism of the entire flora and selected families and genera in a search for commonalities. Methods The elevational patterns of endemism for the entire Ecuadorean vascular plant flora, for twenty‐seven selected families, and for twenty‐four selected genera based on the Catalogue of Vascular Plants of Ecuador were analysed. Results Elevational patterns of endemism were non‐random at all taxonomic levels but there was no common elevational pattern. Rather, the study groups showed a wide variety of independent patterns at all taxonomic levels. Most groups had hump‐shaped patterns with maxima at different elevations and mostly at the same or at higher elevations than the maxima of species richness. The overall flora showed highest endemism in the narrowest and most fragmented elevational belts, presumably because of the consequent fragmentation of species populations. Main conclusions Patterns of endemism appear to be influenced both by taxon‐specific ecological traits (e.g. life form, reproduction, dispersal, demography, spatial population structure, competitive ability) in their specific interaction with historical processes and by environmental factors such as topographical fragmentation. The degree to which these influences become visible along the elevational gradient are determined by which combination of species is analysed: for a given genus or family, taxon‐specific traits dominate the patterns, for the entire flora taxon‐specific patterns are blurred by averaging and the signal of topography emerges. Beyond the elevational gradient as such, this study shows that the frequently stated assumption that given biogeographical settings lead to similar patterns of endemism among different taxa is wrong.     

The Effects of the Porosity of a Support and of Attachment on the Mode of Action of Immobilized Endopolygalacturonase

Endopolygalacturonase of Aspergillus sp. was immobilized by three different methods; viz. (a) via amino groups, (b) via carboxyl groups and (c) by means of epoxy groups to a nonporous microparticular silicon dioxide (Cabosil), functionalized by 3-(amino)-propyl groups and 3-(2',3'-epoxypropoxy)-propyl groups, respectively. The conjugates were compared in their mode of action with corresponding immobilized preparations based on microporous ceramics. The binding via amino groups and via carboxyl groups lead, by itself, to changes in the mode of action of the enzyme, consisting of a decrease in randomness of glycosidic linkage splitting. The changes were greater in microporous support conjugates due to additional size-exclusion effects. The action pattern of endopolygalacturonase bound by means of epoxy groups was modulated exclusively by the porosity of the support, whereas the binding alone did not play any role.     

Pattern formation underlying phytochrome-mediated anthocyanin synthesis in the cotyledons ofSinapis alba L.

The ability to respond to phytochrome (P_fr, the far-red light absorbing from of phytochrome) with anthocyanin synthesis appears first in some marginal regions of the abaxial epidermis of the mustard cotyledons and from there spreads gradually over the entire tissue (transient phase). The pertinent pattern is independent of environmental influences such as light quality and nutritional culture conditions. The competence for P_fr in the epidermal cells, with regard to the initial action of P_fr (concerning anthocyanin synthesis), appears considerably earlier than the ability for actual anthocyanin synthesis. An electron microscopical study of the ultrastructural changes occurring in vacuoles and plastids of the epidermal cells during the transient phase showed that a correlation only exists between the differentiation of central cell vacuoles, originating from the aleurone vacuoles, and the appearance of the ability to accumulate anthocyanin. It is suggested that the formation of a central cell vacuole is a prerequisite for anthocyanin accumulation in the epidermal cells of the mustard seedling cotyledons.Abbreviations P_r, P_fr red and far-red absorbing forms of phytochrome - HS Hoagland's nutrient solution     

Anthochlor pigments and floral UV patterns in the genus Bidens

The occurrence of floral UV absorption-reflection patterns in Bidens laevis is due to a spatial segregation of anthochlor pigments in the flower head. Interspecific, UV pattern polymorphism within this genus falls generally along taxonomic (sectional) lines.     

Advanced-level Biology—A Possible Approach

Teachers' conscious priorities in selecting topics for teaching rarely include the ‘biology/social science interfaces’; neither are many usually aware of the existence and implications of ‘hidden ideologies’ in the curriculum. This paper gives several examples of such interfaces, and stresses the point that only by redirecting the education of teachers can their awareness and priorities be suitably altered.     

Functional relationships between dental attrition and the helicoidal plane

Several quantitative techniques were used to describe and analyze the development of the helicoidal curve of the dentition in a pre-contact sample of 326 native Indians from British Columbia. Results were compared with studies of occlusal patterns in other populations, and anatomical-functional features of the helicoidal pattern were abstracted and generalized. The features that define the helicoidal pattern were found to develop with attrition. The pattern itself, and the complex which produces it, probably have been selected for because they produce an occlusion with an efficient cutting edge and a total complex that provides maximum resistance to the masticatory forces. Studies focusing on the developmental nature of occlusal patterns in early hominid populations would be beneficial in developing a model of the evolution of the helicoidal pattern in modern man.     

Turnover of O-Glucosides of Dihydrozeatin and Dihydrozeatin-9-riboside During the Cell Growth Cycle of Photoautotrophic Cell Suspension Cultures of Chenopodium rubrum

The cellular levels of O-glucosides of ³H-(diH)Z and ³H-(diH)[9R]Z, the major short-term metabolites of ³H-(diH)Z having been exogenously supplied to photoautotrophically growing suspension cell cultures of Chenopodium rubrum, decreased significantly during further culture, irrespective of whether the cells were maintained in the stationary phase or were transferred to conditions restoring cell divison. Metabolism of both compounds was more pronounced during the active growth phase than during the stationary phase. The O-glucosides were converted preferentially to polar compounds of as yet unknown nature, which were partly excreted into the medium. The cellular pools of both glycosides remained compartmented within the vacuole. In contrast to the O-glycosides, the small cellular pools of the aglycones ³H-(diH)Z and ³H-(diH)[9R]Z maintained their level during the experimental period of 30 days. Small amounts of the glucosides, as well as of the aglycones, were recovered from the medium and could have resulted from the lysis of a few cells. The results demonstrate, for the first time, that O-glucosides of cytokinins are not irreversibly deposited within the vacuole of plant cells but may serve to maintain a small, but more or less constant pool of extra-vacuolar, presumably cytosolic, aglycones. (DiH)Z and its derivatives could be demonstrated to be endogenous cytokinins of Chenopodium rubrum suspension cultured cells occurring along with those of the isopentenyladenine and zeatin types.