Comparing the energy landscapes for native folding and aggregation of PrP

Protein sequences are evolved to encode generally one folded structure, out of a nearly infinite array of possible folds. Underlying this code is a funneled free energy landscape that guides folding to the native conformation. Protein misfolding and aggregation are also a manifestation of free-energy landscapes. The detailed mechanisms of these processes are poorly understood, but often involve rare, transient species and a variety of different pathways. The inherent complexity of misfolding has hampered efforts to measure aggregation pathways and the underlying energy landscape, especially using traditional methods where ensemble averaging obscures important rare and transient events. We recently studied the misfolding and aggregation of prion protein by examining 2 monomers tethered in close proximity as a dimer, showing how the steps leading to the formation of a stable aggregated state can be resolved in the single-molecule limit and the underlying energy landscape thereby reconstructed. This approach allows a more quantitative comparison of native folding versus misfolding, including fundamental differences in the dynamics for misfolding. By identifying key steps and interactions leading to misfolding, it should help to identify potential drug targets. Here we describe the importance of characterizing free-energy landscapes for aggregation and the challenges involved in doing so, and we discuss how single-molecule studies can help test proposed structural models for PrP aggregates.     

Anatomical site of pheromone accumulation and temporal pattern of pheromone emission in the ambrosia beetle Megaplatypus mutatus

Megaplatypus mutatus (Chapuis) is a native South American ambrosia beetle that attacks live hardwood trees (e.g. Populus spp.), causing important economic losses to commercial plantations. Male beetles release the main components of the sex pheromone, namely (+)‐6‐methyl‐5‐hepten‐2‐ol [(+)‐sulcatol, or retusol] and 6‐methyl‐5‐hepten‐2‐one (sulcatone), when colonizing suitable hosts. The hindgut is shown to be the anatomical site of pheromone accumulation within males, the enantiomeric composition of sulcatol in this tissue is 99%‐(+) and sulcatol is first detectable in this tissue on days 1–2 after gallery initiation. Peak accumulation of sulcatol occurs on days 5–12 after gallery initiation. Trace quantities of sulcatone are also observed during the same period. Both pheromone components are present in male emissions from three host species (Populus×canadensis, Populus alba and Casuarina stricta) between days 2 and 12 after gallery initiation, although sulcatone is always present in low concentrations. The temporal patterns of sulcatol and sulcatone accumulation or storage in male M. mutatus correspond to the temporal patterns of emission.     

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.     

Effects of trichomes on the behavior and distribution of Platyprepia virginalis caterpillars

Trichomes are an important physical resistance mechanism of plants, as they reduce insect herbivore movement, feeding, and digestion. However, we know little about how trichomes influence herbivore distributions and populations. We conducted laboratory and field experiments to evaluate the preferences of Platyprepia virginalis (Boisduval) (Lepidoptera: Arctiidae) caterpillars to natural and manipulated densities of trichomes on their primary food, Lupinus arboreus Sims (Fabaceae). We then conducted field surveys to determine whether variation in trichome density among lupine bushes affected caterpillar spatial distribution on the landscape. Platyprepia virginalis caterpillars preferred lupine leaves with fewer trichomes in choice and no‐choice experiments. In the field, caterpillar feeding damage was found more often on leaves with fewer trichomes. These preferences scaled up to the level of bushes in the landscape such that more caterpillars were found on bushes with lower trichome densities than on bushes with higher trichome densities. This is one of few studies to show the potential for trichome density to influence herbivore population size and distribution in a natural system at a landscape level. The results are consistent with trichomes functioning as a resistance mechanism with consequences for herbivore choice, performance, and distribution.     

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     

pathmatrix: a geographical information system tool to compute effective distances among samples

pathmatrix is a tool used to compute matrices of effective geographical distances among samples using a least‐cost path algorithm. This program is dedicated to the study of the role of the environment on the spatial genetic structure of populations. Punctual locations (e.g. individuals) or zones encompassing sample data points (e.g. demes) are used in conjunction with a species‐specific friction map representing the cost of movement through the landscape. Matrices of effective distances can then be exported to population genetic software to test, for example, for isolation by distance. pathmatrix is an extension to the geographical information system (GIS) software arcview 3.x.     

Effects of Organic Solvents on the Coupling Between ATP Hydrolysis and Sliding of Microtubules in Axonemes from Chlamydomonas Flagella

ABSTRACT. The effects of organic solvents on the ATPase activity and the sliding disintegration of axonemes from Chlamydomonas were investigated. The axonemal ATPase was markedly activated by methanol accompanying with marked inhibition of the sliding disintegration of axonemes. On the contrary, glycerol inhibited the ATPase activity without serious inhibition of the sliding disintegration. As far as the axonemes are not irreversibly denatured by extremely high concentration of solvents, the effects of solvents both on the ATPase and the ability of sliding are reversible. Therefore, the inhibition of sliding accompanied by the activation of ATPase is probably due to an inability to couple the hydrolysis of ATP to sliding between dynein and microtubule in the presence of methanol. The axonemal ATPase was less sensitive to vanadate inhibition after exposure to methanol. This indicates that methanol makes the dyneinADP.Pi complex unstable and increases product release. On the other hand, glycerol and ethylene glycol seem to stabilize the force generation responsible for the sliding through stabilizing the dynein.ADP.Pi complex.