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1.
Miguel Jiménez-Valdés Héctor Godínez-Alvarez Javier Caballero Rafael Lira 《Economic botany》2010,64(2):149-160
Population Dynamics of
Agave marmorata
Roezl. under Two Contrasting Management Systems in Central Mexico. This paper evaluates the impacts of traditional management on the population dynamics of Agave marmorata, a multipurpose, useful species that is dominant in the Zapotitlán Salinas Valley, Puebla, Mexico. During 2002–2003 and 2003–2004,
we constructed matrix models for two populations—one unmanaged, the other subject to plant extraction and cutting of flowering
stalks. We also conducted prospective (elasticity) and retrospective (life table response experiments) analyses. Overall,
the unmanaged population had higher finite rates of increase (λ) than the managed one. This variation in λ was the result
of a decrease in the individual growth and fecundity in the managed population. Survival and growth were the demographic processes
with the highest contribution to λ in the unmanaged population, while survival was the most important in the managed one.
Our results suggest that management and plant extraction practices could be having negative effects on the population dynamics
of this plant species. Recommendations are provided in order to promote positive effects on its vital rates and regeneration
capacity. 相似文献
2.
Due to the conventional distinction between ecological (rapid) and evolutionary (slow) timescales, ecological and population models have typically ignored the effects of evolution. Yet the potential for
rapid evolutionary change has been recently established and may be critical to understanding how populations persist in changing
environments. In this paper we examine the relationship between ecological and evolutionary dynamics, focusing on a well-studied
experimental aquatic predator-prey system (Fussmann et al., 2000, Science, 290, 1358–1360; Shertzer et al., 2002, J. Anim. Ecol., 71, 802–815; Yoshida et al., 2003, Nature, 424, 303–306). Major properties of predator-prey cycles in this system are determined by ongoing evolutionary dynamics in the
prey population. Under some conditions, however, the populations tend to apparently stable steady-state densities. These are
the subject of the present paper. We examine a previously developed model for the system, to determine how evolution shapes
properties of the equilibria, in particular the number and identity of coexisting prey genotypes. We then apply these results
to explore how evolutionary dynamics can shape the responses of the system to ‘management’: externally imposed alterations
in conditions. Specifically, we compare the behavior of the system including evolutionary dynamics, with predictions that
would be made if the potential for rapid evolutionary change is neglected. Finally, we posit some simple experiments to verify
our prediction that evolution can have significant qualitative effects on observed population-level responses to changing
conditions. 相似文献
3.
Insulin-secreting β-cells, located within the pancreatic islets of Langerhans, are excitable cells that produce regular bursts of action potentials
when stimulated by glucose. This system has been the focus of mathematical investigation for two decades, spawning an array
of mathematical models. Recently, a new class of models has been introduced called ‘phantom bursters’ [Bertram et al. (2000) Biophys. J.
79, 2880–2892], which accounts for the wide range of burst frequencies exhibited by islets via the interaction of more than
one slow process. Here, we describe one implementation of the phantom bursting mechanism in which intracellular Ca2+ controls the oscillations through both direct and indirect negative feedback pathways. We show how the model dynamics can
be understood through an extension of the fast/slow analysis that is typically employed for bursting oscillations. From this
perspective, the model makes use of multiple degrees of freedom to generate the full range of bursting oscillations exhibited
by β-cells. The model also accounts for a wide range of experimental phenomena, including the ubiquitous triphasic response to
the step elevation of glucose and responses to perturbations of internal Ca2+ stores. Although it is not presently a complete model of all β-cell properties, it demonstrates the design principles that we anticipate will underlie future progress in β-cell modeling. 相似文献
4.
Linearized oscillations in population dynamics 总被引:6,自引:0,他引:6
A linearized oscillation theorem due to Kulenović, Ladas and Meimaridou (1987,Quart. appl. Math.
XLV, 155–164) and an extension of it are applied to obtain the oscillation of solutions of several equations which have appeared
in population dynamics. They include the logistic equation with several delays, Nicholson's blowflies model as described by
Gurney, Blythe and Nisbet (1980,Nature, Lond.
287, 17–21) and the Lasota-Wazewska model of the red blood cell supply in an animal. We also developed a linearized oscillation
result for difference equations and applied it to several equations taken from the biological literature. 相似文献
5.
Concomitant resistance is a tumor growth dynamic which results when the growth of a second tumor implant is inhibited by the
presence of the first. Recently, we modeled tumor growth in the presence of a regenerating liver after partial hepatectomy
(Michelson and Leith,Bull. Math. Biol.
57, 345–366, 1995), with an interlocking pair of growth control triads to account for the accelerated growth observed in both
tissues. We also modeled tumor dormancy and recurrence as a dynamic equilibrium achieved between proliferating and quiescent
subpopulations. In this paper those studies are extended to initially model the concomitant resistance case.
Two interlocking model systems are proposed. In one an interactive competition between the tumor implants is described, while
in the other purely proportional growth inhibition is described. The equilibria and dynamics of each system when the coefficients
are held constant are presented for three subcases of model parameters.
We show that the dynamic called concomitant resistance can be real or apparent, and that if the model coefficients are held
constant, the only way to truly achieve concomitant resistance is by forcing one of the tumors into total quiescence. If this
is the true state of the inhibited implant, then a non-constant recruitment signal is required to insure regrowth when the
inhibitor mass is excised. We compare these theoretical results to a potential explanation of the phenomenon provided by Prehn
(Cancer Res.
53, 3266–3269, 1993). 相似文献
6.
In recent years, it has become clear that the neuronal nicotinic acetylcholine receptor (nAChR) is a valid target in the treatment
of a variety of diseases, including Alzheimer’s disease, anxiety, and nicotine addiction. As with most membrane proteins,
information on the three-dimensional (3D) structure of nAChR is limited to data from electron microscopy, at a resolution
that makes the application of structure-based design approaches to develop specific ligands difficult. Based on a high-resolution
crystal structure of AChBP, homology models of the extracellular domain of the neuronal rat and human nAChR subtypes α4β2
and α7 (the subtypes most abundant in brain) were built, and their stability assessed with molecular dynamics (MD). All models
built showed conformational stability over time, confirming the quality of the starting 3D model. Lipophilicity and electrostatic
potential studies performed on the rat and human α4β2 and α7 nicotinic models were compared to AChBP, revealing the importance
of the hydrophobic aromatic pocket and the critical role of the α-subunit Trp—the homolog of AChBP-Trp 143—for ligand binding.
The models presented provide a valuable framework for the structure-based design of specific α4β2 nAChR subtype ligands aimed
at improving therapeutic and diagnostic applications.
Figure Electrostatic surface potential of the binding site cavity of the neuronal nicotinic acetylcholine receptor (nAChR). Nicotinic
models performed with the MOLCAD program: a rat α7, b rat α4β2, c human α7, d human α4β2. All residues labeled are part of the α7 (a,c) or α4 (b,d) subunit with the exception of Phe 117, which belongs to subunit β2 (d). Violet Very negative, blue negative, yellow neutral, red very positive 相似文献
7.
The cortical medial superior temporal area (MST) is essential for the normal execution of smooth pursuit eye movements. Many
pursuit-related neurons (visual-tracking neurons = VT neurons) in the lateral part of area MST (MSTl) are responsive to retinal
image slip (r) as well as to eye (e) and head velocity (h) with similar preferred directions (isodirectionality). We show, by running a connectionist network with VT neuron-like elements, that an assembly of MSTl-VT neurons is able to
reconstruct target motion in world-centered coordinates (t′). When t′ is fed into a subsequent model stage, converting t′ into gaze velocity (g′) with varying contributions of e and h, the overall model is able to account for many of the salient properties of visually guided pursuit including the consequences
of MSTl lesions. However, the analysis of the MSTl network also clearly indicates that isodirectionality is not a prerequisite
for its performance. The investigation of a second model suggests that isodirectionality indeed does not result from functional
but from developmental constraints. This second model is a connectionist network with hidden units, which similar to MSTl-VT
neurons receive input from modality specific units encoding retinal slip, eye and head velocity. After training this network
to offer t′ as output, two subsets of hidden units emerged, one exhibiting isodirectionality, but not the other. Since only isodirectional
hidden units contributed to the flow of information, the preponderance of isodirectional MSTl-VT neurons might be the result
of developmental pruning, eliminating the second group.
Received: 17 April 1998 / Accepted in revised form: 28 July 1998 相似文献
8.
A formalism based on window automata is proposed as a method to analyse complex population dynamics. The method is applied
to a model of the immune network (Weisbuch, G.et al., 1990.J. theor. Biol.
146, 483–499), and used to predict which attractor the system reaches after antigenic stimulation, as a function of the parameters.
The attractors of the dynamics are interpreted in terms of immune conditions such as vaccination or tolerance. Scaling laws
that define the regimes in the parameter space corresponding to the specific attractor reached under antigenic stimulation
are derived. 相似文献
9.
The ability to switch attention from one aspect of an object to another or in other words to switch the “attentional set”
as investigated in tasks like the “Wisconsin Card Sorting Test” is commonly referred to as cognitive flexibility. In this work we present a biophysically detailed neurodynamical model which illustrates the neuronal base of the processes
related to this cognitive flexibility. For this purpose we conducted behavioral experiments which allow the combined evaluation of different aspects of set shifting
tasks: uninstructed set shifts as investigated in Wisconsin-like tasks, effects of stimulus congruency as investigated in
Stroop-like tasks and the contribution of working memory as investigated in “Delayed-Match-to-Sample” tasks. The work describes
how general experimental findings are usable to design the architecture of a biophysical detailed though minimalistic model
with a high orientation on neurobiological findings and how, in turn, the simulations support experimental investigations.
The resulting model is able to account for experimental and individual response times and error rates and enables the switch
of attention as a system inherent model feature: The switching process suggested by the model is based on the memorization
of the visual stimuli and does not require any synaptic learning. The operation of the model thus demonstrates with at least
a high probability the neuronal dynamics underlying a key component of human behavior: the ability to adapt behavior according
to context requirements—cognitive flexibility.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
Action Editor: Peter Dayan 相似文献
10.
V. S. Ivlev 《Bulletin of mathematical biology》1965,27(1):215-222
The survival rate of fishes in their earlier stages of development and the influencing factors present one of the most fundamental
problems of fish population dynamics. After I. Hjort's (Cons. L.'explor. Ner.,20, 3–228, 1914) work, there have been many investigators in this field and there is no doubt about the very important role
of ova and larvae mortality in the fate of a given fish generation.
Less clear are the ideas concerning factors determining the high mortality of fishes in their earlier stages of development;
especially the factor of food supply of larvae during the period of transition to exogenic nutrition. The value of this factor
has been estimated differently from different points of view. For example, R. J. H. Beverton and S. J. Holt (On the Dynamics of Exploited Fish Population, 1957) have given to the food supply factor its deserved importance. On the other hand, T. V. Dekhnik (Trudy Sevastopolskoi Biologicheskoi Stantsii,13, 216–244, 1960;Ibid.,14, 222–243, 1961) has proved in her investigations that at least for pelagic larvae of Black Sea fishes there is an excessive
amount of food, and that therefore food cannot play an important role in larva survival.
Not wanting to stop to review the literature of the problem (see Dekhnik,Trudy Sevastopolskoi Biologicheskoi Stantsii,13, 216–244, 1960), we will only remark that the problem as a whole needs further investigation. Not only new data are needed,
but also methods for following up analysis have to be worked out. 相似文献
11.
Feng XJ Shea-Brown E Greenwald B Kosut R Rabitz H 《Journal of computational neuroscience》2007,23(3):265-282
Deep brain stimulation (DBS) of the subthalamic nucleus, typically with periodic, high frequency pulse trains, has proven
to be an effective treatment for the motor symptoms of Parkinson’s disease (PD). Here, we use a biophysically-based model
of spiking cells in the basal ganglia (Terman et al., Journal of Neuroscience, 22, 2963–2976, 2002; Rubin and Terman, Journal of Computational Neuroscience, 16, 211–235, 2004) to provide computational evidence that alternative temporal patterns of DBS inputs might be equally effective as the standard
high-frequency waveforms, but require lower amplitudes. Within this model, DBS performance is assessed in two ways. First,
we determine the extent to which DBS causes Gpi (globus pallidus pars interna) synaptic outputs, which are burstlike and synchronized in the unstimulated Parkinsonian state, to cease their pathological
modulation of simulated thalamocortical cells. Second, we evaluate how DBS affects the GPi cells’ auto- and cross-correlograms.
In both cases, a nonlinear closed-loop learning algorithm identifies effective DBS inputs that are optimized to have minimal
strength. The network dynamics that result differ from the regular, entrained firing which some previous studies have associated
with conventional high-frequency DBS. This type of optimized solution is also found with heterogeneity in both the intrinsic
network dynamics and the strength of DBS inputs received at various cells. Such alternative DBS inputs could potentially be
identified, guided by the model-free learning algorithm, in experimental or eventual clinical settings.
Action Editor: Steven J. Schiff
Xiao-Jiang Feng and Eric Shea-Brown contributed equally to this work. 相似文献
12.
Cashman DJ Buscaglia R Freyer MW Dettler J Hurley LH Lewis EA 《Journal of molecular modeling》2008,14(2):93-101
G-Quadruplex and i-Motif-forming sequences in the promoter regions of several oncogenes show promise as targets for the regulation
of oncogenes. In this study, molecular models were created for the c-MYC NHE-III1 (nuclease hypersensitivity element III1) from two 39-base complementary sequences. The NHE modeled here consists of single folded conformers of the polypurine intramolecular
G-Quadruplex and the polypyrimidine intramolecular i-Motif structures, flanked by short duplex DNA sequences. The G-Quadruplex
was based on published NMR structural data for the c-MYC 1:2:1 loop isomer. The i-Motif structure is theoretical (with five
cytosine–cytosine pairs), where the central intercalated cytosine core interactions are based on NMR structural data obtained
for a tetramolecular [d(A2C4)4] model i-Motif. The loop structures are in silico predictions of the c-MYC i-motif loops. The porphyrin meso-tetra(N-methyl-4-pyridyl)porphine
(TMPyP4), as well as the ortho and meta analogs TMPyP2 and TMPyP3, were docked to six different locations in the complete
c-MYC NHE. Comparisons are made for drug binding to the NHE and the isolated G-Quadruplex and i-Motif structures. NHE models
both with and without bound cationic porphyrin were simulated for 100 ps using molecular dynamics techniques, and the non-bonded
interaction energies between the DNA and porphyrins calculated for all of the docking interactions.
Figure Molecular models of the average structure of the final 20 ps of the molecular dynamics simulation of the c-MYC NHE-III1 (nuclease hypersensitivity element III1) “silencer” element. The G-Quadruplex structure is at the top-center, and the i-Motif is at the bottom-center of each picture.
a “Rotation #1” of the G-Quadruplex, with the T15 loop at the top and rear and the G19/A20 loop at the top and front of the picture. b “Rotation #2” of the G-Quadruplex, with the T15 loop at the top and front of the image, and the G19/A20 loop at the front and adjacent to the G-Quadruplex/i-Motif interface 相似文献
13.
This article focuses on the analysis of coastal fish communities along the Norwegian Skagerrak coast. Species numbers are
estimated based on annual samples of the fish communities within 12 fjords from 1953 to 1994. On this basis, a community dynamics
model (incorporating both community-intrinsic and community-extrinsic processes) was developed and analyzed. This model is
then discussed on the basis of other community models available through the literature, both phenomenologically oriented and
process-oriented models.
Received: January 17, 2002 / Accepted: May 13, 2002
Acknowledgments We thank Dr. Masakado Kawata for the invi-tation to present this paper at the 19th Symposium of the Society of Population
Ecology held in Yamagata, Japan, October 26–28, 2001: “Evolution of Biodiversity: Theories and Facts.” Valuable input was
provided after the presentation at this meeting, which we greatly appreciated. The reformulation of the model in terms of
ΔS was kindly suggested to us by Prof. Joan Roughgarden. Thanks to Dr. Hildegunn Viljugrein for advice on the BUGS analyses
and to two anonymous reviewers for constructive comments. This work has been supported by grants from the Norwegian Science
Council (NFR).
Correspondence to:N.C. Stenseth 相似文献
14.
15.
The dynamics of the nucleobase and the ribose moieties in a 14-nt RNA cUUCGg hairpin-loop uniformly labeled with 13C and 15N were studied by 13C spin relaxation experiments. R1, R1ρ and the 13C-{1H} steady-state NOE of C6 and C1′ in pyrimidine and C8 and C1′ in purine residues were obtained at 298 K. The relaxation data were analyzed by the model-free formalism to yield dynamic
information on timescales of pico-, nano- and milli-seconds. An axially symmetric diffusion tensor with an overall rotational
correlation time τc of 2.31±0.13 ns and an axial ratio of 1.35±0.02 were determined. Both findings are in agreement with hydrodynamic calculations.
For the nucleobase carbons, the validity of different reported 13C chemical shift anisotropy values (Stueber, D. and Grant, D. M., 2002 J. Am. Chem. Soc. 124, 10539–10551; Fiala et al., 2000 J. Biomol. NMR 16, 291–302; Sitkoff, D. and Case, D. A., 1998 Prog. NMR Spectroscopy 32, 165–190) is discussed. The resulting dynamics are in agreement with the structural features of the cUUCGg motif in that
all residues are mostly rigid (0.82 < S2 < 0.96) in both the nucleobase and the ribose moiety except for the nucleobase of U7, which is protruding into solution (S2 = 0.76). In general, ribose mobility follows nucleobase dynamics, but is less pronounced. Nucleobase dynamics resulting from
the analysis of 13C relaxation rates were found to be in agreement with 15N relaxation data derived dynamic information (Akke et al., 1997 RNA 3, 702–709).
Electronic supplementary material Electronic supplementary material is available for this article at
and accessible for authorised users. 相似文献
16.
A. W. E. Dilg Giovanna Mincione Klaus Achterhold Olga Iakovleva Matthias Mentler Claudio Luchinat Ivano Bertini F. G. Parak 《Journal of biological inorganic chemistry》1999,4(6):727-741
4 S4]3 + and the reduced [Fe4S4]2 + clusters in the high-potential iron protein I from Ectothiorhodospira halophila were measured in a temperature range from 5 K to 240 K. EPR measurements and 57Fe electron-nuclear double resonance (ENDOR) experiments were carried out with the oxidized protein. In the oxidized state
the cluster has a net spin S = 1/2 and is paramagnetic. As common in [Fe4S4]3 + clusters, the M?ssbauer spectrum was simulated with two species contributing equally to the absorption area: two Fe3 + atoms couple to the “ferric-ferric” pair, and one Fe2 + and one Fe3 + atom give the “ferric-ferrous pair”. For the simulation of the M?ssbauer spectrum, g-values were taken from EPR measurements. A-tensor components were determined by 57Fe ENDOR experiments that turned out to be a necessary source of estimating parameters independently. In order to obtain a
detailed agreement of M?ssbauer and ENDOR data, electronic relaxation has to be taken into account. Relaxing the symmetry
condition in a way that the electric field gradient tensor does not coincide with g- and A-tensors yielded an even better agreement of experimental and theoretical M?ssbauer spectra. Spin-spin and spin-lattice relaxation
times were estimated by pulsed EPR; the former turned out to be the dominating mechanism at T = 5 K. Relaxation times measured by pulsed EPR and obtained from the M?ssbauer fit were compared and yield nearly identical
values. The reduced cluster has one additional electron and has a diamagnetic (S = 0) ground state. All the four irons are indistinguishable in the M?ssbauer spectrum, indicating a mixed-valence state of
Fe2.5 + for each.
Received: 15 February 1999 / Accepted: 31 August 1999 相似文献
17.
Two models of binary tree growth are examined in terms of the Strahler order branching ratio (Rb) and the types of vertex produced during growth, and their inter-relationship. The sequential growth model is that described
by Van Pelt and Verwer (1985,Bull. math. Biol.
47, 323–336) in which random growth occurs according to attributed probabilities on terminal or internal segments, one branch
at a time. This model generates values ofRb≥3. The synchronous growth model is new and permits more than one segment to branch at a time, again randomly with attributed
probabilities. This model generates values ofRb≥2 and in particular, when only terminal branching is permitted, gives 2≤Rb<3. Such a model might explain the branching in the human bronchial tree, in which 2.5≤Rb≤2.8. Our synchronous model is an alternative to the centrifugal-order-dependent sequential model of Van Pelt and Verwer. 相似文献
18.
Organisms often shown enhanced growth during recovery from starvation, and can even overtake continuously fed conspecifics
(overcompensation). In an earlier paper (Ecology
84, 2777–2787), we studied the relative role played by hyperphagia and resource allocation in producing overcompensation in
juvenile (non-reproductive) animals. We found that, although hyperphagia always produces growth compensation, overcompensation
additionally requires protein allocation control which routes assimilate preferentially to structure during recovery. In this
paper we extend our model to cover reproductively active individuals and demonstrate that growth rate overcompensation requires
a similar combination of hyperphagia and allocation control which routes the part of enhanced assimilation not used for reproduction
preferentially towards structural growth. We compare the properties of our dynamic energy budget model with an earlier proposal,
due to Kooijman, which we extend to include hyperphagia. This formulation assumes that the rate of allocation to reserves
is controlled by instantaneous feeding rate, and one would thus expect that an extension to include hyperphagia would not
predict growth overcompensation. However, we show that a self-consistent representation of the hyperphagic response in Kooijman’s
model overrides its fundamental dynamics, leading to preferential allocation to structural growth during recovery and hence
to growth overcompensation. 相似文献
19.
The tachykinins are a family of gastrointestinal peptides comprising eight members: substance P, neurokinin A, neurokinin
B, eledoisin, physalemin, uperolein, kassinin and phyllomedusin. Consensus dynamics was carried out on an
ensemble
of seven tachykinins to determine the binding conformation of the common C-terminal fragment: Phe-X-Gly-Leu-Met-NH
2
,the ’message sequence’ of tachykinins. Three binding modes for the C-terminal pentapeptide were determined. The first binding
conformation is folded due to an intramolecular H-bond between the NH of the variable residue (X) and CO of Met. Other features
include γ-bends at both the variable amino acid (X) and at Gly. The global minimum of the simulation has this conformation
for the C-terminal pentapeptide. The other two binding modes have slightly higher energies. The second is chiefly characterized
by a β-turn around the segment X-Gly-Leu-Met, with additional β-bends at the variable amino acid (X) and Met. The final binding
conformation is composed of β-bends around the variable amino acid (X) and Leu, and a ’pseudo’ γ-bend at the terminal Met.
This paper was presented at the MBU Silver Jubilee Symposium on Structural Biology and 24th Annual Meeting of the Indian Biophysical
Society held at Indian Institute of Science, Bangalore, Dec. 9–12, 1996. 相似文献
20.
Lim Amareth Saderholm Matthew J. Kroll Mathias Yan Yibing Erickson Bruce W. Guy Philippe A. Anderegg Robert J. Makhov Alexander M. Griffith Jack D. 《International journal of peptide research and therapeutics》1999,6(1):3-14
Summary The inverse protein-folding problem has been explored by designing de novo the betabellin target structure (a 64-residue β-sandwich
protein), synthesizing a 32-residue peptide chain (HSLTAKIpkLTFSIAphTYTCAVpkYTAKVSH, wherep=DPro,k=DLys, andh=DHis) that might fold into this structure, and studying how its disulfide-bridged form (betabellin 15D) folds in 10 mM ammonium
acetate with and without Cu2+. Circular dichroic spectropolarimetry indicated that at pH 5.8, 6.4, or 6.7 betabellin 15D exhibited β-sheet structure in
the presence of Cu2+ but not in its absence. Electrospray mass spectrometry demonstrated that at pH 6.3 each molecule of betabellin 15D bound
one or two Cu(II) ions. Electron microscopy showed that at pH 6.7 betabellin 15D formed short broad fibrils in the presence
of Cu2+ but not in its absence. The observed width of the fibrils (7±2 nm) was consistent with the width (6.8nm) of a structural
model of a fibril that contained two adjacent rows of betabellin 15D β-sandwiches joined lengthwise by multiple intersheet
hydrogen bonds and widthwise by multiple Cu(II)-imidazole bonds. Electron paramagnetic resonance spectrometry revealed that
some pairs of Cu(II) ions in a Cu(II)/betabellin 15D complex were magnetically coupled, which is consistent with the structural
model of the Cu(II)/betabellin 15D fibril. 相似文献