Interaction between Hsc70 and DnaJ homologues: relationship between Hsc70 polymerization and ATPase activity.

We previously found that, in the presence of ATP, DnaJ homologues catalytically induce formation of a metastable Hsc70 polymer and, similarly, the DnaJ homologue auxilin catalytically induces formation of a metastable Hsc70-clathrin basket complex. Since this suggests that the induction of metastable complexes, which form in ATP but dissociate in ADP, may be a general property of DnaJ homologues, in the present study we investigated in more detail the ability of DnaJ homologues to induce polymerization of Hsc70. This study shows that DnaJ homologues induce polymerization of Hsc70 at the same rate as they induce an initial burst of Hsc70 ATPase activity, showing that polymerization is a specific effect of DnaJ homologue binding to Hsc70. However, polymerization does not always accompany the initial burst of ATPase activity. The dependence of the rates of ATPase activity and polymerization on DnaJ homologue concentration shows that DnaJ homologues bind very weakly to Hsc70 in the presence of ATP and do not bind at all in ADP. Surprisingly, however, under certain conditions the rate of polymerization appears to be independent of Hsc70 concentration, suggesting that polymerization is a first-order reaction, perhaps occurring when two Hsc70 molecules bind to a single DnaJ molecule and then shift their binding to each other. We propose that both the polymerization of Hsc70 by DnaJ homologues and the presentation of substrate by DnaJ homologues to Hsc70 involve the bringing of substrate into proximity with Hsc70 and then independently inducing rapid ATP hydrolysis to cause formation of a metastable Hsc70-substrate complex.     

Selection for High Oridonin Yield in the Chinese Medicinal Plant Isodon (Lamiaceae) Using a Combined Phylogenetics and Population Genetics Approach

Oridonin is a diterpenoid with anti-cancer activity that occurs in the Chinese medicinal plant Isodon rubescens and some related species. While the bioactivity of oridonin has been well studied, the extent of natural variation in the production of this compound is poorly known. This study characterizes natural variation in oridonin production in order to guide selection of populations of Isodon with highest oridonin yield. Different populations of I. rubescens and related species were collected in China, and their offspring were grown in a greenhouse. Samples were examined for oridonin content, genotyped using 11 microsatellites, and representatives were sequenced for three phylogenetic markers (ITS, rps16, trnL-trnF). Oridonin production was mapped on a molecular phylogeny of the genus Isodon using samples from each population as well as previously published Genbank sequences. Oridonin has been reported in 12 out of 74 species of Isodon examined for diterpenoids, and the phylogeny indicates that oridonin production has arisen at least three times in the genus. Oridonin production was surprisingly consistent between wild-collected parents and greenhouse-grown offspring, despite evidence of gene flow between oridonin-producing and non-producing populations of Isodon. Additionally, microsatellite genetic distance between individuals was significantly correlated with chemical distance in both parents and offspring. Neither heritability nor correlation with genetic distance were significant when the comparison was restricted to only populations of I. rubescens, but this result should be corroborated using additional samples. Based on these results, future screening of Isodon populations for oridonin yield should initially prioritize a broad survey of all species known to produce oridonin, rather than focusing on multiple populations of one species, such as I. rubescens. Of the samples examined here, I. rubescens or I. japonicus from Henan province would provide the best source of oridonin.     

An automatic device to record the force necessary to compensate plant movements

A device, which automatically and continuously keeps moving plants in fixed positions, has been constructed. The apparatus is based on optical detection of any movements of the plant organ under study. The plant organ is kept in the desired position by means of wires, and the force necessary to apply to the wires to achieve this is recorded. The force reflects any tendency of the plant organ to move. The system is controlled by an Apple II computer. The device can work in one or two dimensions and record compensation forces in a wide range. In the experiments mentioned below, the magnitude of the forces necessary to keep the plants in a fixed position was of the order of 10^-4N.
Circadian leaf movements of Oxalis regnellii Mig. were studied in the device. The leaf rhythm continued, although the leaflets were clamped and the light input on the leaf therefore constant. Circumnutation of hypocotyls of Helianthus annus L. cv. Californicus were drastically reduced in amplitude when the hypocotyls were kept in vertical position by the wires. Since the gravitropic input signal to this system was zeroed by the equipment, the results demonstrated that in the absence of gravitropic inputs the circumnutation reactions drastically diminish. This confirmed that circumnutations of these hypocotyls are influenced by gravity. Finally, the apparatus was used to study phototropic reactions: By clamping phototropically stimulated coleoptiles of Avena sativa L. cv. Seger no gravitational stimulations were involved and the phototropic reaction without interference from gravity could be studied.     

Fish and fisheries in hot water: What is happening and how do we adapt?

Rapid climate changes are currently driving substantial reorganizations of marine ecosystems around the world. A key question is how these changes will alter the provision of ecosystem services from the ocean, particularly from fisheries. To answer this question, we need to understand not only the ecological dynamics of marine systems, but also human adaptation and feedbacks between humans and the rest of the natural world. In this review, we outline what we have learned from research primarily in continental shelf ecosystems and fishing communities of North America. Key findings are that marine animals are highly sensitive to warming and are responding quickly to changes in water temperature, and that such changes are often happening faster than similar processes on land. Changes in species distributions and productivity are having substantial impacts on fisheries, including through changing catch compositions and longer distances traveled for fishing trips. Conflicts over access to fisheries have also emerged as species distributions are no longer aligned with regulations or catch allocations. These changes in the coupled natural-human system have reduced the value of ecosystem services from some fisheries and risk doing so even more in the future. Going forward, substantial opportunities for more effective fisheries management and operations, marine conservation, and marine spatial planning are likely possible through greater consideration of climate information over time-scales from years to decades.     

Dynamic combinatorial libraries of artificial repeat proteins

Repeat proteins are found in almost all cellular systems, where they are involved in diverse molecular recognition processes. Recent studies have suggested that de novo designed repeat proteins may serve as universal binders, and might potentially be used as practical alternative to antibodies. We describe here a novel chemical methodology for producing small libraries of repeat proteins, and screening in parallel the ligand binding of library members. The first stage of this research involved the total synthesis of a consensus-based three-repeat tetratricopeptide (TPR) protein (～14 kDa), via sequential attachment of the respective peptides. Despite the effectiveness of the synthesis and ligation steps, this method was found to be too demanding for the production of proteins containing variable number of repeats. Additionally, the analysis of binding of the individual proteins was time consuming. Therefore, we designed and prepared novel dynamic combinatorial libraries (DCLs), and show that their equilibration can facilitate the formation of TPR proteins containing up to eight repeating units. Interestingly, equilibration of the library building blocks in the presence of the biologically relevant ligands, Hsp90 and Hsp70, induced their oligomerization into forming more of the proteins with large recognition surfaces. We suggest that this work presents a novel simple and rapid tool for the simultaneous screening of protein mixtures with variable binding surfaces, and for identifying new binders for ligands of interest.     

BioMOCA—a Boltzmann transport Monte Carlo model for ion channel simulation

With the recent availability of high-resolution structural information for several key ion channel proteins and large-scale computational resources, Molecular Dynamics has become an increasingly popular tool for ion channel simulation. However, the CPU requirements for simulating ion transport on time scales relevant to conduction still exceed the resources presently available. To address this problem, we have developed Biology Monte Carlo (BioMOCA), a three-dimensional (3D) coarse-grained particle ion channel simulator based on the Boltzmann Transport Monte Carlo (BTMC) methodology. Although this approach is widely employed in the engineering community to study charge transport in electron devices, its application to molecular biology and electrolytes in general is new and hence must be validated. The pair correlation function, which is a measure of the microscopic structure of matter, provides a suitable benchmark to compare the BTMC method against the well-established Equilibrium Monte Carlo (EMC) approach. For validation purposes BioMOCA is used to simulate several simple homogeneous equilibrium electrolytes at concentrations of physiological interest. The ion–ion pair correlation functions computed from these simulations compare very well with those obtained from EMC simulations. We also demonstrate several performance-improving techniques that result in a several-fold speed-up without compromising the pair correlation function. BioMOCA is then used to perform full 3D simulations of ion transport in the gramicidin A channel in situ in a membrane environment, as well as to study the link between the electrostatic and dielectric properties of the protein and the channel's selectivity.     

Nucleosome core particle structure and structural changes in solution

The radius of gyration, Rg, of chicken erythrocyte nucleosome core particles, was found to be 4.56 (+/- 0.07) nm by small-angle X-ray scattering, independent of particle concentration and of NaCl concentration between 0.1 M and 0.6 M-NaCl. The large, positive, second virial coefficient, A2, from particle concentration dependence (but independent of NaCl concentration) in small-angle X-ray scattering may indicate non-electrostatic repulsive ordering over large distances. Density contrast variation in equilibrium sedimentation with a small probe (sucrose) and a larger probe (gamma-cyclodextrin) yields good results for core particle hydration in the first instance, and for an estimate of the total particle volume in the second instance.