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  • 1
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    Multiscale Modeling of Double-Helical DNA and RNA: A Unification through Lie Groups (2012)
    American Chemical Society (ACS)
    Details
    Publication Date: 2012-06-08
    Description: The Journal of Physical Chemistry B DOI: 10.1021/jp2126015
    Electronic ISSN: 1520-5207
    Topics: Chemistry and Pharmacology , Physics
    Published by American Chemical Society (ACS)
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  • 2
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    The challenge of modelling nitrogen management at the field scale: simulation and sensitivity analysis of N 2 O fluxes across nine experimental sites using DailyDayCent (2014)
    Institute of Physics (IOP)
    Details
    Publication Date: 2014-09-09
    Description: The United Kingdom currently reports nitrous oxide emissions from agriculture using the IPCC default Tier 1 methodology. However Tier 1 estimates have a large degree of uncertainty as they do not account for spatial variations in emissions. Therefore biogeochemical models such as DailyDayCent (DDC) are increasingly being used to provide a spatially disaggregated assessment of annual emissions. Prior to use, an assessment of the ability of the model to predict annual emissions should be undertaken, coupled with an analysis of how model inputs influence model outputs, and whether the modelled estimates are more robust that those derived from the Tier 1 methodology. The aims of the study were (a) to evaluate if the DailyDayCent model can accurately estimate annual N 2 O emissions across nine different experimental sites, (b) to examine its sensitivity to different soil and climate inputs across a number of experimental sites and (c) to examine the influence of uncertainty i...
    Print ISSN: 1748-9318
    Electronic ISSN: 1748-9326
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering
    Published by Institute of Physics (IOP)
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  • 3
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    A diversity of paracrine signals sustains molecular circadian cycling in suprachiasmatic nucleus circuits [Neuroscience] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-08-24
    Description: The suprachiasmatic nucleus (SCN) is the principal circadian pacemaker of mammals, coordinating daily rhythms of behavior and metabolism. Circadian timekeeping in SCN neurons revolves around transcriptional/posttranslational feedback loops, in which Period (Per) and Cryptochrome (Cry) genes are negatively regulated by their protein products. Recent studies have revealed, however, that these “core loops” also rely upon cytosolic and circuit-level properties for sustained oscillation. To characterize interneuronal signals responsible for robust pacemaking in SCN cells and circuits, we have developed a unique coculture technique using wild-type (WT) “graft” SCN to drive pacemaking (reported by PER2::LUCIFERASE bioluminescence) in “host” SCN deficient either in elements of neuropeptidergic signaling or in elements of the core feedback loop. We demonstrate that paracrine signaling is sufficient to restore cellular synchrony and amplitude of pacemaking in SCN circuits lacking vasoactive intestinal peptide (VIP). By using grafts with mutant circadian periods we show that pacemaking in the host SCN is specified by the genotype of the graft, confirming graft-derived factors as determinants of the host rhythm. By combining pharmacological with genetic manipulations, we show that a hierarchy of neuropeptidergic signals underpins this paracrine regulation, with a preeminent role for VIP augmented by contributions from arginine vasopressin (AVP) and gastrin-releasing peptide (GRP). Finally, we show that interneuronal signaling is sufficiently powerful to maintain circadian pacemaking in arrhythmic Cry-null SCN, deficient in essential elements of the transcriptional negative feedback loops. Thus, a hierarchy of paracrine neuropeptidergic signals determines cell- and circuit-level circadian pacemaking in the SCN.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 4
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    Equivalence in yield from marine reserves and traditional fisheries management (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-05-29
    Description: Marine reserves have been proposed as a remedy for overfishing and declining marine biodiversity, but concern that reserves would inherently reduce yields has impeded their implementation. It was found that management of fisheries through reserves and management through effort control produce identical yields under a reasonable set of simplifying assumptions corresponding to a broad range of biological conditions. Indeed, for populations with sedentary adults (invertebrates and reef fishes), reserves have important advantages for sustainability, making marine reserves the preferred management approach.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hastings -- Botsford -- New York, N.Y. -- Science. 1999 May 28;284(5419):1537-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Environmental Science and Policy, Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, CA 95616, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10348743" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Ecology. The lion and the lamb find closure (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-24
    Description: Interactions between enemies and their victims are found in all ecological communities. But what has puzzled ecologists is how victims and enemies coexist together for long periods of time without all of the victims being killed off. In a Perspective, Hastings explains a new model (Keeling et al.), which shows that variation in the distribution of victim and enemy species acts as a stabilizing factor in interactions between them.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hastings, A -- New York, N.Y. -- Science. 2000 Dec 1;290(5497):1712-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Environmental Science and Policy, University of California, Davis, CA 95616, USA. amhastings@ucdavis.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11186394" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Computer Simulation ; *Ecosystem ; *Host-Parasite Interactions ; Insects/*parasitology/*physiology ; *Models, Biological ; Models, Statistical ; Population Dynamics ; Stochastic Processes ; Time Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Extinction risk depends strongly on factors contributing to stochasticity (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-07-04
    Description: Extinction risk in natural populations depends on stochastic factors that affect individuals, and is estimated by incorporating such factors into stochastic models. Stochasticity can be divided into four categories, which include the probabilistic nature of birth and death at the level of individuals (demographic stochasticity), variation in population-level birth and death rates among times or locations (environmental stochasticity), the sex of individuals and variation in vital rates among individuals within a population (demographic heterogeneity). Mechanistic stochastic models that include all of these factors have not previously been developed to examine their combined effects on extinction risk. Here we derive a family of stochastic Ricker models using different combinations of all these stochastic factors, and show that extinction risk depends strongly on the combination of factors that contribute to stochasticity. Furthermore, we show that only with the full stochastic model can the relative importance of environmental and demographic variability, and therefore extinction risk, be correctly determined. Using the full model, we find that demographic sources of stochasticity are the prominent cause of variability in a laboratory population of Tribolium castaneum (red flour beetle), whereas using only the standard simpler models would lead to the erroneous conclusion that environmental variability dominates. Our results demonstrate that current estimates of extinction risk for natural populations could be greatly underestimated because variability has been mistakenly attributed to the environment rather than the demographic factors described here that entail much higher extinction risk for the same variability level.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Melbourne, Brett A -- Hastings, Alan -- England -- Nature. 2008 Jul 3;454(7200):100-3. doi: 10.1038/nature06922.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA. brett.melbourne@colorado.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18596809" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Environment ; *Extinction, Biological ; Female ; Fishes ; Life Cycle Stages ; Male ; Models, Statistical ; Risk Factors ; Stochastic Processes ; Tribolium/*physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 7
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    Strong effect of dispersal network structure on ecological dynamics (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-10-22
    Description: A central question in ecology with great importance for management, conservation and biological control is how changing connectivity affects the persistence and dynamics of interacting species. Researchers in many disciplines have used large systems of coupled oscillators to model the behaviour of a diverse array of fluctuating systems in nature. In the well-studied regime of weak coupling, synchronization is favoured by increases in coupling strength and large-scale network structures (for example 'small worlds') that produce short cuts and clustering. Here we show that, by contrast, randomizing the structure of dispersal networks in a model of predators and prey tends to favour asynchrony and prolonged transient dynamics, with resulting effects on the amplitudes of population fluctuations. Our results focus on synchronization and dynamics of clusters in models, and on timescales, more appropriate for ecology, namely smaller systems with strong interactions outside the weak-coupling regime, rather than the better-studied cases of large, weakly coupled systems. In these smaller systems, the dynamics of transients and the effects of changes in connectivity can be well understood using a set of methods including numerical reconstructions of phase dynamics, examinations of cluster formation and the consideration of important aspects of cyclic dynamics, such as amplitude.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holland, Matthew D -- Hastings, Alan -- England -- Nature. 2008 Dec 11;456(7223):792-4. doi: 10.1038/nature07395. Epub 2008 Oct 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Environmental Science and Policy, University of California, Davis, One Shields Avenue, Davis, California 95616, USA. mdholland@ucdavis.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18931656" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Ecosystem ; Food Chain ; *Models, Biological ; Population Dynamics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 8
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    Mathematical and computational challenges in population biology and ecosystems science (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-01-17
    Description: Mathematical and computational approaches provide powerful tools in the study of problems in population biology and ecosystems science. The subject has a rich history intertwined with the development of statistics and dynamical systems theory, but recent analytical advances, coupled with the enhanced potential of high-speed computation, have opened up new vistas and presented new challenges. Key challenges involve ways to deal with the collective dynamics of heterogeneous ensembles of individuals, and to scale from small spatial regions to large ones. The central issues-understanding how detail at one scale makes its signature felt at other scales, and how to relate phenomena across scales-cut across scientific disciplines and go to the heart of algorithmic development of approaches to high-speed computation. Examples are given from ecology, genetics, epidemiology, and immunology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Levin, S A -- Grenfell, B -- Hastings, A -- Perelson, A S -- AI28433/AI/NIAID NIH HHS/ -- RR06555/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1997 Jan 17;275(5298):334-43.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8994023" target="_blank"〉PubMed〈/a〉
    Keywords: Acquired Immunodeficiency Syndrome/virology ; *Allergy and Immunology ; Animals ; Biological Evolution ; Communicable Diseases/transmission ; *Computational Biology ; Computer Simulation ; *Ecology ; *Epidemiology ; *Genetics ; Humans ; Models, Biological ; *Virology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    Metapopulation persistence with age-dependent disturbance or succession (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-09-13
    Description: Simple metapopulation models with random disturbances are used in species conservation or management, relying on the condition for persistence that the per-patch colonization rate be greater than the per-patch extinction rate. For a general model incorporating the role of succession or patch age-dependent extinction, I show that persistence requires the per-patch colonization rate to be greater than the inverse of mean patch age, where age is the time since the patch became available for colonization. Because mean patch age can be arbitrarily large relative to the extinction rate, currently persisting metapopulations may be persisting despite small colonization rates, and management approaches that do not consider the role of mean patch age may unnecessarily doom populations to extinction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hastings, Alan -- New York, N.Y. -- Science. 2003 Sep 12;301(5639):1525-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Environmental Science and Policy, University of California, One Shields Avenue, Davis, CA 95616, USA. amhastings@ucdavis.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12970563" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anura ; *Conservation of Natural Resources ; *Ecosystem ; *Environment ; Forestry ; Mathematics ; Models, Biological ; Models, Statistical ; Population Dynamics ; Probability ; Time Factors ; Trees
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Mathematics and biology. A bright future for biologists and mathematicians? (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hastings, Alan -- Palmer, Margaret A -- New York, N.Y. -- Science. 2003 Mar 28;299(5615):2003-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Environmental Science and Policy, University of California, Davis, CA 95616, USA. amhastings@ucdavis.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12663907" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biology ; Communicable Diseases/epidemiology ; Conservation of Natural Resources ; Disease Outbreaks ; Ecosystem ; Humans ; *Mathematics ; *Models, Biological ; Molecular Motor Proteins/physiology ; Organisms, Genetically Modified ; Population Dynamics ; Stochastic Processes
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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