Effects of 3′-deoxyadenosine triphosphate on in vitro RNA synthesis of plant RNA-dependent RNA polymerases

3′-deoxyadenosine triphosphate inhibited $\text{in}\text{vitro}$ [³H]UMP incorporation by RNA-dependent RNA polymerases from tobacco and cowpea plants. The inhibition of [³H]UMP incorporation could be reversed by simultaneous addition of higher ATP concentrations but not with increasing concentrations of UTP or when excess ATP was added 10 min after the inhibitor. These results suggest 3′-deoxyadenosine triphosphate competes specifically with ATP in reaction mixtures and results in premature termination of RNA synthesis $\text{in}\text{vitro}$ by RNA-dependent RNA polymerase.     

Sequence–structure relationships in RNA loops: establishing the basis for loop homology modeling

The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence–structure relationships in loops. Loops differing by <25% in sequence identity fold into very similar structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.     

The physical basis of alpha waves in the electroencephalogram and the origin of the “Berger effect”

Synchronised activity, differing in phase in different populations of neurons, plays an important role in existing theories on the function of brain oscillations (e.g., temporal correlation hypothesis). A prerequisite for this synchronisation is that stimuli are capable of affecting (resetting) the phase of brain oscillations. Such a change in the phase of brain waves is also assumed to underlie the Berger effect: when observers open their eyes, the amplitude of EEG oscillations in the alpha band (8–13 Hz) decreases significantly. This finding is usually thought to involve a desynchronisation of activity in different neurons. For functional interpretations of brain oscillations in the visual system, it therefore seems to be crucial to find out whether or not the phase of brain oscillations can be affected by visual stimuli. To answer this question, we investigated whether alpha waves are generated by a linear or a nonlinear mechanism. If the mechanism is linear – in contrast to nonlinear ones – phases cannot be reset by a stimulus. It is shown that alpha-wave activity in the EEG comprises both linear and nonlinear components. The generation of alpha waves basically is a linear process and flash-evoked potentials are superimposed on ongoing alpha waves without resetting their phase. One nonlinear component is due to light adaptation, which contributes to the Berger effect. The results call into question theories about brain-wave function based on temporal correlation or event-related desynchronisation.Electronic Supplementary Material: Supplementary material is available for this article at     

A note on the fine structure of the Ochromonas danica “tail”

Summary The fine structure of the Ochromonas danica tail is detailed. The microtubules, microtubule anchoring structures, posterior swelling, surface vesicles, and in some instances cup shape of the tail end are described and used to explain the behavior of the organism when attached to surfaces.Aided by a grant GB 20825 from the National Science Foundation.     

The evolutionary basis of leaf senescence: method to the madness?

Recent studies on the differential expression of genes associated with leaf senescence support the long-standing interpretation of plant senescence as an organized, genetically controlled process. Sequence identities of genes that are differentially expressed in senescing leaves indicate roles in the salvage of nutrients. By considering this salvage function as the selected trait and the degeneration and death of the tissue a pleiotropic consequence of nutrient redistribution, the process of leaf senescence can be reconciled with evolutionary theories on the origins of senescence in animals.     

The structure of the α-keratin microfibril

Quantitative measurements of the intensity of the meridional reflections in the X-ray-diffraction pattern of alpha-keratin are shown to be consistent with a microfibril structure in which a surface lattice with an axially projected period around 200 A is subject to a periodic interruption with an axially projected period of 470 A. Taken in conjunction with recent evidence on the chemical structure of alpha-keratin and other intermediate filaments this finding enables an elaboration to be made of a model proposed earlier by RDB Fraser, TP MacRae, & E Suzuki (J. Mol. Biol. 108, 435-452, 1976) for the alpha-helical framework of the microfibril. The disposition and connectivity of the helical segments suggested here provides a straightforward explanation of a number of recent physicochemical and electron-microscopical observations on intermediate filaments and provides a starting point for the development of models for the framework of other intermediate filaments.     

The effects of cholesterol and β-sitosterol on the structure of saturated diacylphosphatidylcholine bilayers

The structures of DMPC and DPPC bilayers in unilamellar liposomes, in the presence of 33.3 mol% cholesterol or the plant sterol β-sitosterol, have been studied by small-angle neutron scattering. The bilayer thickness d _L increases in a similar way for both sterols. The repeat distance in multilamellar liposomes, as determined by small-angle X-ray diffraction, is larger in the presence of β-sitosterol than in the presence of cholesterol. We observe that each sterol modifies the interlamellar water layer differently, cholesterol reducing its thickness more efficiently than β-sitosterol, and conclude that cholesterol suppresses bilayer undulations more effectively than β-sitosterol.     

The effects of prostaglandin F2α on the fine structure of the corpus luteum of the pregnant hamster

Summary The commonest intracellular organelle characteristic of the Phylum Cnidaria or Coelenterata (Subclass Zoantharia) is the spirocyst. Based on scanning and transmission electron microscopy of the tentacles of sea anemones and corals, it appears that the tip of the spirocyst is either exposed to the environment or covered by a thin plasma membrane and often has a pebbled or knobby appearance. Surrounding the spirocyst tip is a ring-like structure which seems to be formed by the junction of the enclosing cell (the spirocyte) and the tip of the spirocyst. The spirocyst thread is continuous with the capsule wall and emerges from within the apical ring during discharge. No ciliary structures appear to be associated with spirocysts. Instead, two different types of microvilli have been found: short microvilli on the spirocyte itself and long microvilli furnished by the cell or cells surrounding the spirocyte. The significance of these findings is discussed in relation to the reception of stimuli for spirocyst discharge.Thanks are due Dr. Cadet Hand for the use of facilities of the Bodega Marine Laboratory of the University of California and Dr. R.K. Thompson, P. Nemanic, H. Sampson, F. Doroshow, E. Chang and B. Miller for expert technical assistance. The use of the facilities of the Electron Microscope Laboratory and the Electronics Research Laboratory of the University of California and the Electron Microscope Laboratory of the Florida State University is gratefully acknowledged. Part of this work was made possible by NSF Grant # GB-40547 to the senior author.     

Saponins and Phylogeny: Example of the “Gypsogenin group” Saponins

The chemical structure of triterpenoid saponins is quite complicated, especially the glucuronide oleanane-type triterpene carboxylic acid 3,28-bidesmosides (GOTCAB) saponins. Moreover, triterpenoid saponins are numerous as a result of this complicated structure. This review tries to explain this diversity in terms of plant classification and phylogeny. The study focuses on the three main successive steps of the biosynthetic pathway of the triterpenoid saponins: cyclisation, oxidation and glycosylation showing the relationship between triterpenols and sterols in terms of cell membrane evolution and the importance of which metabolic intermediates involved as aglycones of the triterpenoid saponins, represented progressively less and less in the advanced groups of the plant kingdom as they are more and more oxidised. This oxidation seems to reflect a better adaptation to new environmental conditions of some of these groups. By their enormous chemical diversity, the triterpenoid saponins seem to be good candidates to study the phylogeny of the flowering plants. A first attempt is given using recent advances in botanical classification for the orders and families by the Angiosperm Phylogenic Group (APG). This study was simplified in the first step focusing only on the “gypsogenin group” of the GOTCAB saponins. For example, as a result, these compounds are mainly concentrated in advanced groups such as Caryophyllideae, primitive Rosideae and Asterideae.     

When is bigger better? The effects of group size on the evolution of helping behaviours

Understanding the evolution of sociality in humans and other species requires understanding how selection on social behaviour varies with group size. However, the effects of group size are frequently obscured in the theoretical literature, which often makes assumptions that are at odds with empirical findings. In particular, mechanisms are suggested as supporting large‐scale cooperation when they would in fact rapidly become ineffective with increasing group size. Here we review the literature on the evolution of helping behaviours (cooperation and altruism), and frame it using a simple synthetic model that allows us to delineate how the three main components of the selection pressure on helping must vary with increasing group size. The first component is the marginal benefit of helping to group members, which determines both direct fitness benefits to the actor and indirect fitness benefits to recipients. While this is often assumed to be independent of group size, marginal benefits are in practice likely to be maximal at intermediate group sizes for many types of collective action problems, and will eventually become very small in large groups due to the law of decreasing marginal returns. The second component is the response of social partners on the past play of an actor, which underlies conditional behaviour under repeated social interactions. We argue that under realistic conditions on the transmission of information in a population, this response on past play decreases rapidly with increasing group size so that reciprocity alone (whether direct, indirect, or generalised) cannot sustain cooperation in very large groups. The final component is the relatedness between actor and recipient, which, according to the rules of inheritance, again decreases rapidly with increasing group size. These results explain why helping behaviours in very large social groups are limited to cases where the number of reproducing individuals is small, as in social insects, or where there are social institutions that can promote (possibly through sanctioning) large‐scale cooperation, as in human societies. Finally, we discuss how individually devised institutions can foster the transition from small‐scale to large‐scale cooperative groups in human evolution.