Structural Analysis and Stochastic Modelling Suggest a Mechanism for Calmodulin Trapping by CaMKII

Activation of CaMKII by calmodulin and the subsequent maintenance of constitutive activity through autophosphorylation at threonine residue 286 (Thr286) are thought to play a major role in synaptic plasticity. One of the effects of autophosphorylation at Thr286 is to increase the apparent affinity of CaMKII for calmodulin, a phenomenon known as “calmodulin trapping”. It has previously been suggested that two binding sites for calmodulin exist on CaMKII, with high and low affinities, respectively. We built structural models of calmodulin bound to both of these sites. Molecular dynamics simulation showed that while binding of calmodulin to the supposed low-affinity binding site on CaMKII is compatible with closing (and hence, inactivation) of the kinase, and could even favour it, binding to the high-affinity site is not. Stochastic simulations of a biochemical model showed that the existence of two such binding sites, one of them accessible only in the active, open conformation, would be sufficient to explain calmodulin trapping by CaMKII. We can explain the effect of CaMKII autophosphorylation at Thr286 on calmodulin trapping: It stabilises the active state and therefore makes the high-affinity binding site accessible. Crucially, a model with only one binding site where calmodulin binding and CaMKII inactivation are strictly mutually exclusive cannot reproduce calmodulin trapping. One of the predictions of our study is that calmodulin binding in itself is not sufficient for CaMKII activation, although high-affinity binding of calmodulin is

Can Ptilinopus greyii (Columbidae) Disperse Seeds in New Caledonia’s Dry Forests?

v. ill. 23 cm.QuarterlyConservation of endangered habitats of South Pacific islands is partially dependent on activity of seed dispersers. In consuming fruits, animals can spread seeds from parent plants to distant sites, thus contributing to plant regeneration and colonization of new sites. In the dry forests of New Caledonia, the red-bellied fruit-dove, Ptilinopus greyii, is a potential disperser of many fleshyfruited species. Trials with a captive bird showed that gut passage enhanced seed germination for Diospyros fasciculosa and Mimusops elengi but not for Vitex cf. collina, compared with whole fruits. Gut passage did not shorten duration of seed dormancy, which is consistent with evidence of a simple deinhibition effect for D. fasciculosa and M. elengi. Minimum Retention Time (MRT) of seeds in the gut differed significantly between the three tree species, from a mean of 17.4 min for D. fasciculosa to a mean of 52.4 min for M. elengi. These times are longer than observed foraging times in fruiting trees, potentially making this fruit-dove an effective seed disperser

Delivery Drones - Just a Hype? Towards Autonomous Air Mobility Services at Scale

While hype often arises around emerging technologies, delivery drones have received a significant share of attention in recent years. A variety of applications for drone networks formed, from delivering medical goods to drone-delivered pizza. Nevertheless, high expectations did not yet result in a widespread deployment of drones to improve logistic networks. We conducted semi-structured interviews with drone and aviation experts to derive a taxonomy of challenges for autonomous drone operations and gain practical insight into promising solution approaches that could transform the current hype into sound business models. Our findings comprise a multitude of operational, technical, social and legal issues that have not been identified in literature. Societal adaption and the development and interaction with AI-based systems pose a major challenge to provide autonomous air mobility services in the near future

Calcium Input Frequency, Duration and Amplitude Differentially Modulate the Relative Activation of Calcineurin and CaMKII

NMDA receptor dependent long-term potentiation (LTP) and long-term depression (LTD) are two prominent forms of synaptic plasticity, both of which are triggered by post-synaptic calcium elevation. To understand how calcium selectively stimulates two opposing processes, we developed a detailed computational model and performed simulations with different calcium input frequencies, amplitudes, and durations. We show that with a total amount of calcium ions kept constant, high frequencies of calcium pulses stimulate calmodulin more efficiently. Calcium input activates both calcineurin and Ca2+/calmodulin-dependent protein kinase II (CaMKII) at all frequencies, but increased frequencies shift the relative activation from calcineurin to CaMKII. Irrespective of amplitude and duration of the inputs, the total amount of calcium ions injected adjusts the sensitivity of the system to calcium input frequencies. At a given frequency, the quantity of CaMKII activated is proportional to the total amount of calcium. Thus, an input of a small amount of calcium at high frequencies can induce the same activation of CaMKII as a larger amount, at lower frequencies. Finally, the extent of activation of CaMKII signals with high calcium frequency is further controlled by other factors, including the availability of calmodulin, and by the potency of phosphatase inhibitors

Generating and visualizing a soccer knowledge base

This demo abstract describes the SmartWeb Ontology-based Information Extraction System (SOBIE). A key feature of SOBIE is that all information is extracted and stored with respect to the SmartWeb ontology. In this way, other components of the systems, which use the same ontology, can access this information in a straightforward way. We will show how information extracted by SOBIE is visualized within its original context, thus enhancing the browsing experience of the end user

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

Background: Quantitative models of biochemical and cellular systems are used to answer a variety of questions in the biological sciences. The number of published quantitative models is growing steadily thanks to increasing interest in the use of models as well as the development of improved software systems and the availability of better, cheaper computer hardware. To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. Ideally, the models stored in these repositories should be extensively tested and encoded in community-supported and standardised formats. In addition, the models and their components should be cross-referenced with other resources in order to allow their unambiguous identification. Description: BioModels Database http://www.ebi.ac.uk/biomodels/ is aimed at addressing exactly these needs. It is a freely-accessible online resource for storing, viewing, retrieving, and analysing published, peer-reviewed quantitative models of biochemical and cellular systems. The structure and behaviour of each simulation model distributed by BioModels Database are thoroughly checked; in addition, model elements are annotated with terms from controlled vocabularies as well as linked to relevant data resources. Models can be examined online or downloaded in various formats. Reaction network diagrams generated from the models are also available in several formats. BioModels Database also provides features such as online simulation and the extraction of components from large scale models into smaller submodels. Finally, the system provides a range of web services that external software systems can use to access up-to-date data from the database. Conclusions: BioModels Database has become a recognised reference resource for systems biology. It is being used by the community in a variety of ways; for example, it is used to benchmark different simulation systems, and to study the clustering of models based upon their annotations. Model deposition to the database today is advised by several publishers of scientific journals. The models in BioModels Database are freely distributed and reusable; the underlying software infrastructure is also available from SourceForge https://sourceforge.net/projects/biomodels/ under the GNU General Public License

Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters

<p>Abstract</p> <p>Background</p> <p>Modellers using the MWC allosteric framework have often found it difficult to validate their models. Indeed many experiments are not conducted with the notion of alternative conformations in mind and therefore do not (or cannot) measure relevant microscopic constant and parameters. Instead, experimentalists widely use the Adair-Klotz approach in order to describe their experimental data.</p> <p>Results</p> <p>We propose a way of computing apparent Adair-Klotz constants from microscopic association constants and allosteric parameters of a generalised concerted model with two different states (<it>R </it>and <it>T</it>), with an arbitrary number of non-equivalent ligand binding sites. We apply this framework to compute Adair-Klotz constants from existing models of calmodulin and hemoglobin, two extreme cases of the general framework.</p> <p>Conclusion</p> <p>The validation of computational models requires methods to relate model parameters to experimentally observable quantities. We provide such a method for comparing generalised MWC allosteric models to experimentally determined Adair-Klotz constants.</p

Decelerating molecules with microwave fields

We here report on the experimental realization of a microwave decelerator for neutral polar molecules, suitable for decelerating and focusing molecules in high-field-seeking states. The multi-stage decelerator consists of a cylindrical microwave cavity oscillating on the TE 11n mode, with n=12 electric field maxima along the symmetry axis. By switching the microwave field on and off at the appropriate times, a beam of state-selected ammonia molecules with an incident mean velocity of 25 m/s is guided while being spatially focussed in the transverse direction and bunched in the forward direction. Deceleration from 20.0 m/s to 16.9 m/s and acceleration from 20.0 m/s to 22.7 m/s is demonstrated.Comment: 4 Pages, 3 Figure

Neighbor predation linked to natural competence fosters the transfer of large genomic regions in Vibrio cholerae

Natural competence for transformation is a primary mode of horizontal gene transfer. Competent bacteria are able to absorb free DNA from their surroundings and exchange this DNA against pieces of their own genome when sufficiently homologous. However, the prevalence of non-degraded DNA with sufficient coding capacity is not well understood. In this context, we previously showed that naturally competent Vibrio cholerae use their type VI secretion system (T6SS) to actively acquire DNA from non-kin neighbors. Here, we explored the conditions of the DNA released through T6SS-mediated killing versus passive cell lysis and the extent of the transfers that occur due to these conditions. We show that competent V. cholerae acquire DNA fragments with a length exceeding 150 kbp in a T6SS-dependent manner. Collectively, our data support the notion that the environmental lifestyle of V. cholerae fosters the exchange of genetic material with sufficient coding capacity to significantly accelerate bacterial evolution