Ball and socket figures between secretory vesicles in mammary epithelial cells

Summary Interaction of adjacent secretory vesicles through ball and socket figures was observed in milk secreting mammary epithelial cells preserved by quick freezing without chemical fixation. Membranes of adjacent vesicles appeared to be fused together. Such vesicle-vesicle interactions have been described in chemically fixed tissues, but it has been argued that these interactions may have been fixation artifacts. Ball and socket figures in quick-frozen cells were smaller than those in chemically fixed cells. However, their existence in cells arrested by quick freezing argues that such vesicle-vesicle interactions occur in living cells.     

Algorithms for the automated selection of fragment-like molecules using single-point surface plasmon resonance measurements

Fragment-based approaches have added to the arsenal of tools used to identify novel developable leads for drug discovery with high ligand efficiencies. A variety of label-free technologies have been developed and used throughout the industry for fragment screening. Using surface plasmon resonance (SPR) as a fragment screening platform is a relatively new approach. The miniaturization and automation of this technology has led to an associated problem: the large volume of raw data often makes it challenging to analyze and integrate the results of SPR data into the workflow of project teams engaged in the discovery process in a timely fashion. As such, several sets of equations were derived and implemented on Merck’s intranet to score single sensorgrams to distinguish stable binders from weak or anomalous binders. This set of equations was optimized and validated on simulated data to both capture “fragment-like” behavior from SPR experiments and filter out much of the anomalous behavior commonly observed. It has subsequently been applied successfully to several in-house discovery programs.     

Quantitative analysis of multiple forest disturbances and their compound influences on tree growth in the western U.S.

As the frequencies of extreme weather increase, forest ecosystems experience stronger influences from various disturbances. Previous research focuses on single disturbances or qualitative analysis of overlaid effects from two disturbances. Studies rarely explored the interactions between three or more disturbances, especially mechanisms behind the multiple disturbances. Our study covered four states (Idaho, Montana, Wyoming, and Utah) in the U.S. which shared similar climate patterns and vegetation distributions. We collected 241 chronologies from the International Tree-Ring Data Bank (ITRDB) and our own field expeditions. We assigned each tree ring to eight possible disturbance combinations. From the correlations between tree indices and climate (monthly temperature and total precipitation), the radial growth of tree rings showed a significant positive correlation with summer precipitation and a negative correlation with summer temperature. With three-factor ANOVA and one-way ANOVA, we ranked the impacts of each disturbance and combination of disturbances on tree growth based on tree-ring index; control (1.038) > insect (1.029) > fire (1.008) > fire & insect (0.963) > drought & insect (0.918) > drought (0.890) > drought, fire & insect (0.803) > drought & fire (0.784). We found that in most cases, the combined impact from two disturbances was larger than the impacts from single disturbances with the inclusion-exclusion principle. This research quantitatively revealed the interactions between disturbances and evaluated the effects from a combination of multiple disturbances.     

Distribution of Molecular Scaffolds and R-Groups Isolated from Large Compound Databases

We describe an approach to isolate molecular scaffolds and R-groups from known chemical compounds in order to generate scaffold and R-group databases from two large compound collections, Optiverse^TM and Maybridge^TM. The distributions of molecular scaffolds and R-groups in the parent databases were analysed and compared. We find that a limited number of scaffolds and R-groups account for the majority of database compounds and that most of the scaffolds occur only once or twice in the compound databases. Diversity analysis suggests that the compound and scaffold databases have similar molecular diversity. Implications for library design are discussed.Electronic Supplementary Material available.     

Cell clones and pattern formation: Genetic eye mosaics inDrosophila melanogaster

Summary Genetic eye mosaics ofDrosophila melanogaster have been studied by means of anatomical techniques. Using different cell markers it was found that the ommatidia at the boundaries between phenotypes are composed of cells belonging to different clones. Therefore, the formation of an individual ommatidium does not obey a mechanism based on a common clonal origin of its constituent elements. A statistical analysis of mosaic ommatidia shows that there is a significant tendency for the receptor cellsR2-R5 on the one hand and the receptor cellsR1, R6 andR7 on the other to belong to the same cell clone. The implications of these findings are discussed.     

Morphological differentiation of the central visual cells R7/8 in various regions of the blowfly eye

The central rhabdomeres in the retina of the blowfly Calliphora erythrocephala and the house fly Musca domestica are not structurally uniform. In Calliphora, four classes of central rhabdomeres were found; they are formed by a total of seven types of central visual cells, clearly distinguished by the following structural features: length of the rhabdomeres R7 or R8, position of the nucleus, rhabdomere twist, fine structure in the R7/R8 transition region, and cross-sectional area of the rhabdomeres. In the lateral part of the eye only the most common central-rhabdomere class, ‘sl.’ is present, whereas in the frontal and dorsal parts classes ‘sl’ and ‘ls’ are found in a particular numerical ratio. Near the frontal eye margin the rare class ‘per’ also appears, with two separate rhabdomeres, R7per and R8s; the morphological properties of R7per are midway between those of peripheral and central visual cells. The special ommatidia at the dorsal margin of the eye are characterized by the central rhabdomeres ‘marg’. The known functional properties of the visual cells in the fly eye can be readily assigned to these classes (Table 1, Fig. 12). The non-uniform distribution of the various kinds of central rhabdomeres suggests functional differentiation of the eye region.     

Systematic study on the mechanism of aldehyde oxidation to carboxylic acid by cytochrome P450

The mechanism of aldehyde to carboxylic acid conversion catalyzed by P450 enzymes via a series of reactions was studied systematically for the first time with density functional theory calculations. A two-state reactivity mechanism has been proposed, which can be adopted for many aldehyde oxidation reactions catalyzed by P450 enzymes. The mechanism involves initial hydrogen abstraction as the rate-limiting step and this is followed by steps of oxygen rebound without barriers owing to the quick recombination of the resultant radical species. Meanwhile, in an attempt to explore whether there exist some rules for the hydroxylation of aldehyde substrates by P450, the transition state barriers of the rate-limiting step for a series of aldehyde hydroxylation reactions have been compared. A predictive pattern of extended barrier/bond energy correlation for different hydroxylations of aldehyde substrates by P450 has been established, which was further confirmed to be a reliable reactivity scale by experimental results. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The effect of axial ligands on the reactivity and stability of the oxoferryl moiety in model complexes of Compound I of heme-dependent enzymes

 The contribution of simple inorganic model complexes to the understanding of related processes in biomolecules is demonstrated by a series of Compound I analogs of heme-dependent enzymes. The oxoiron(IV) porphyrin cation radical state in these synthetic complexes is stable enough to be studied by spectroscopic methods as a function of only one variable, the axial ligand trans to the oxoiron bond. Complementary information from kinetic investigations of the reactivity in epoxidation of olefins enables the separation of the thermodynamic and kinetic effects of the axial ligands. The results clearly indicate that epoxidation by these complexes proceeds by two distinguishable steps, which are affected differently by the axial ligands. The first step is electron transfer from the olefin to the ferryl moiety, probably followed by intramolecular charge rearrangement and product release. It is proposed that part of the enhanced oxygenation activities of cytochrome P-450 monooxygenases and chloroperoxidases is due to a lowering of the energy barrier for the second step via participation of their redox-active cysteinate ligand in charge rearrangement. Received and accepted: 7 May 1996