38 research outputs found
Modeling Light Adaptation in Circadian Clock: Prediction of the Response That Stabilizes Entrainment
Periods of biological clocks are close to but often different from the rotation period of the earth. Thus, the clocks of organisms must be adjusted to synchronize with day-night cycles. The primary signal that adjusts the clocks is light. In Neurospora, light transiently up-regulates the expression of specific clock genes. This molecular response to light is called light adaptation. Does light adaptation occur in other organisms? Using published experimental data, we first estimated the time course of the up-regulation rate of gene expression by light. Intriguingly, the estimated up-regulation rate was transient during light period in mice as well as Neurospora. Next, we constructed a computational model to consider how light adaptation had an effect on the entrainment of circadian oscillation to 24-h light-dark cycles. We found that cellular oscillations are more likely to be destabilized without light adaption especially when light intensity is very high. From the present results, we predict that the instability of circadian oscillations under 24-h light-dark cycles can be experimentally observed if light adaptation is altered. We conclude that the functional consequence of light adaptation is to increase the adjustability to 24-h light-dark cycles and then adapt to fluctuating environments in nature
Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements
Acknowledgements Sampling of ruminal digesta was carried out at Scotlandâs Rural College (SRUC) by Laura Nicoll, Lesley Deans and Claire Broadbent. Sequencing using Illumina MiSeq was carried out by Edinburgh Genomics, The University of Edinburgh. Edinburgh Genomics is partly supported through core grants from NERC (R8/H10/56), MRC (MR/K001744/1) and BBSRC (BB/J004243/1). Data were processed using the Maxwell High Performance Computing Cluster of the University of Aberdeen IT Service (www.abdn.ac.uk/staffnet/research/hpc.php), provided by Dell Inc. and supported by Alces Software. Funding This work was funded by the Rural and Environment Science and Analytical Services Division (RESAS) of the Scottish Government as a collaborative HEI project between The University of Aberdeen, The Roslin Institute, and Scotlandâs Rural College (SRUC). The funding body had no role in the design of the study or collection, analysis, or interpretation of data or in writing the manuscript.Peer reviewedPublisher PD
Modularity and predicted functions of the global sponge-microbiome network
Defining the organisation of species interaction networks and unveiling the processes behind their assembly is fundamental to understanding patterns of biodiversity, community stability and ecosystem functioning. Marine sponges host complex communities of microorganisms that contribute to their health and survival, yet the mechanisms behind microbiome assembly are largely unknown. We present the global marine sponge-microbiome network and reveal a modular organisation in both community structure and function. Modules are linked by a few sponge species that share microbes with other species around the world. Further, we provide evidence that abiotic factors influence the structuring of the sponge microbiome when considering all microbes present, but biotic interactions drive the assembly of more intimately associated 'core' microorganisms. These findings suggest that both ecological and evolutionary processes are at play in host-microbe network assembly. We expect mechanisms behind microbiome assembly to be consistent across multicellular hosts throughout the tree of life
Calculation of infrared and Raman vibration modes of magnesite at high pressure by density-functional perturbation theory and comparison with experiments
Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application
An end-to-end platform for chemical science research has been developed that
integrates data from computational and experimental approaches through a modern
web-based interface. The platform offers a highly interactive visualization and
analytics environment that functions well on mobile, laptop and desktop
devices. It offers pragmatic solutions to ensure that large and complex data
sets are more accessible. Existing desktop applications/frameworks were
extended to integrate with high-performance computing (HPC) resources, and
offer command-line tools to automate interaction---connecting distributed teams
to this software platform on their own terms. The platform was developed
openly, and all source code hosted on the GitHub platform with automated
deployment possible using Ansible coupled with standard Ubuntu-based machine
images deployed to cloud machines.
The platform is designed to enable teams to reap the benefits of the
connected web---going beyond what conventional search and analytics platforms
offer in this area. It also has the goal of offering federated instances, that
can be customized to the sites/research performed. Data gets stored using JSON,
extending upon previous approaches using XML, building structures that support
computational chemistry calculations. These structures were developed to make
it easy to process data across different languages, and send data to a
JavaScript web client