共查询到20条相似文献,搜索用时 15 毫秒
1.
In this paper, we present a model that explains the prepatterning of lymphatic vessel morphology in collagen gels. This model
is derived using the theory of two phase rubber material due to Flory and coworkers and it consists of two coupled fourth
order partial differential equations describing the evolution of the collagen volume fraction, and the evolution of the proton
concentration in a collagen implant; as described in experiments of Boardman and Swartz (Circ. Res. 92, 801–808, 2003). Using linear stability analysis, we find that above a critical level of proton concentration, spatial patterns form due
to small perturbations in the initially uniform steady state. Using a long wavelength reduction, we can reduce the two coupled
partial differential equations to one fourth order equation that is very similar to the Cahn–Hilliard equation; however, it
has more complex nonlinearities and degeneracies. We present the results of numerical simulations and discuss the biological
implications of our model.
This work was supported by the Royal Society (London) by the award of a University Research Fellowship. 相似文献
2.
We provide a counter-example to a conjecture of René Thomas on the relationship between negative feedback circuits and stable
periodicity in ordinary differential equation systems (Kaufman et al. in J Theor Biol 248:675–685, 2007). We also prove a weak version of this conjecture by using a theorem of Snoussi. 相似文献
3.
4.
Today, the picture of an evolutionary tree is a very well-known visual image. It is almost impossible to think of the ancestry
and relationships of living beings without it. As natural history museums play a major role in the public understanding of
evolution, they often present a wide variety of evolutionary trees. However, many studies have shown (Baum and Offner 2008; Baum et al. 2005; Catley and Novick 2008; Evans 2009; Gregory 2008; Matuk 2007; Meir et al. 2007b; Padian 2008) that even though evolutionary trees have the potential to engage visitors of natural history museums with the phenomena
of evolution, many of them unwittingly might lead to misunderstandings about the process. As valuable research and educational
institutions, one of the museum’s important missions should be the careful design of their exhibits on evolution considering,
for example, common preconceptions visitors often bring, such as the notion that evolution is oriented from simple toward
complex organisms (incarnating the idea of a single ladder of life amidst the extraordinary diversity of organisms) and that
humans are at the pinnacle of the evolutionary story, as well as na?ve interpretations of phylogenies. Our aim in this article
is to show from history where many of these misunderstandings come from and to determine whether five important Western natural
history museums inadvertently present “problematic” evolutionary trees (which might lead to non-scientific notions). 相似文献
5.
A PDE Model for Imatinib-Treated Chronic Myelogenous Leukemia 总被引:1,自引:0,他引:1
We derive a model for describing the dynamics of imatinib-treated chronic myelogenous leukemia (CML). This model is a continuous
extension of the agent-based CML model of Roeder et al. (Nat. Med. 12(10), 1181–1184, 2006) and of its recent formulation as a system of difference equations (Kim et al. in Bull. Math. Biol. 70(3), 728–744, 2008). The new model is formulated as a system of partial differential equations that describe various stages of differentiation
and maturation of normal hematopoietic cells and of leukemic cells.
An imatinib treatment is also incorporated into the model. The simulations of the new PDE model are shown to qualitatively
agree with the results that were obtained with the discrete-time (difference equation and agent-based) models. At the same
time, for a quantitative agreement, it is necessary to adjust the values of certain parameters, such as the rates of imatinib-induced
inhibition and degradation. 相似文献
6.
With a large number of DNA and protein sequences already known, the crucial question is to find out how the biological function
of these macromolecules is "written" in the sequence of nucleotides or amino acids. Biological processes in any living organism
are based on selective interactions between particular bio-molecules, mostly proteins. The rules governing the coding of a
protein's biological function, i.e. its ability to selectively interact with other molecules, are still not elucidated. In
addition, with the rapid accumulation of databases of protein primary structures, there is an urgent need for theoretical
approaches that are capable of analysing protein structure-function relationships. The Resonant Recognition Model (RRM) [1, 2] is one attempt to identify the selectivity of protein interactions within the amino acid sequence. The RRM [1, 2] is a physico-mathematical approach that interprets protein sequence linear information using digital signal processing methods.
In the RRM the protein primary structure is represented as a numerical series by assigning to each amino acid in the sequence
a physical parameter value relevant to the protein's biological activity. The RRM concept is based on the finding that there
is a significant correlation between spectra of the numerical presentation of amino acids and their biological activity. Once
the characteristic frequency for a particular protein function/interaction is identified, it is possible then to utilize the
RRM approach to predict the amino acids in the protein sequence, which predominantly contribute to this frequency and thus,
to the observed function, as well as to design de novo peptides having the desired periodicities. As was shown in our previous studies of fibroblast growth factor (FGF) peptidic
antagonists [2, 3] and human immunodeficiency virus (HIV) envelope agonists [2, 4], such de novo designed peptides express desired biological function. This study utilises the RRM computational approach to the analysis
of oncogene and proto-oncogene proteins. The results obtained have shown that the RRM is capable of identifying the differences
between the oncogenic and proto-oncogenic proteins with the possibility of identifying the "cancer-causing" features within
their protein primary structure. In addition, the rational design of bioactive peptide analogues displaying oncogenic or proto-oncogenic-like
activity is presented here. 相似文献
7.
Kijimoto-Ochiai S Koda T Suwama T Matsukawa H Fujii M Tomobe K Nishimura M 《Glycoconjugate journal》2008,25(8):787-796
We have already reported that the homogenate of the A/J mouse thymus shows a high sialidase activity at the neutral pH region
and that in both soluble and membrane fractions optimal pH was 6.5–7 (Kijimoto-Ochiai et al., Glycoconj. J., 20:375–384, 2004). In the present study, we investigated the level of sialidase activities in the thymus of the SM/J mouse, a mouse strain
that we know to have a Neu1a allele that reveals a low level of sialidase activity in the liver. We found that while in the A/J thymus the soluble sialidase
activity at pH 6.5 was high, the SM/J thymus lacked all such activity. A QTL analysis of SMXA recombinant inbred strains showed
that soluble sialidase activity correlated well with the D1Mit8/9 marker on chromosome 1. The murine whole DNA-sequence data
and the results of our FISH analysis (Kotani et al., Biochem. Biophys. Res. Comm., 286:250–258, 2001) showed that this location is consistent with the position of Neu2 gene. We confirmed that it is hard to detect the Neu2
enzyme of the SM/J mouse thymus by an anti-Neu2 antibody using a Western blot analysis. We also found that while the mRNA
expression of Neu2 was quite normal in the SM/J mouse liver, it was very low in the SM/J mouse thymus. We therefore conclude
that the lack of soluble sialidase activity in the SM/J mouse thymus is due to the thymus-specific low expression level of
the Neu2 gene. We have previously shown that the sialidase positive cell which contains the Mac-1 and immunoglobulin, and
which is located sparsely in the corticomedullar region or medullary region of the A/J mouse thymus (Kijimoto-Ochiai et al., Glycoconj. J., 20:375–384, 2004). We showed now in this paper that the detection of this cell in the SM/J mouse thymus at pH 7.0 was difficult. We propose,
therefore, to name the cell “Neu-medullocyte”. 相似文献
8.
Brandon W Higgs John Dileo Wenling E Chang Haley B Smith Olivia J Peters Rasha Hammamieh Marti Jett Jordan C Feidler 《BMC microbiology》2006,6(1):48-12
Background
The lack of detailed understanding of the mechanism of action of many biowarfare agents poses an immediate challenge to biodefense efforts. Many potential bioweapons have been shown to affect the cellular pathways controlling apoptosis [1–4]. For example, pathogen-produced exotoxins such as Staphylococcal Enterotoxin B (SEB) and Anthrax Lethal Factor (LF) have been shown to disrupt the Fas-mediated apoptotic pathway [2, 4]. To evaluate how these agents affect these pathways it is first necessary to understand the dynamics of a normally functioning apoptosis network. This can then serve as a baseline against which a pathogen perturbed system can be compared. Such comparisons can expose both the proteins most susceptible to alteration by the agent as well as the most critical reaction rates to better instill control on a biological network. 相似文献9.
Bengt Autzen 《Biology & philosophy》2011,26(4):567-581
Although Bayesian methods are widely used in phylogenetic systematics today, the foundations of this methodology are still
debated among both biologists and philosophers. The Bayesian approach to phylogenetic inference requires the assignment of
prior probabilities to phylogenetic trees. As in other applications of Bayesian epistemology, the question of whether there
is an objective way to assign these prior probabilities is a contested issue. This paper discusses the strategy of constraining
the prior probabilities of phylogenetic trees by means of the Principal Principle. In particular, I discuss a proposal due
to Velasco (Biol Philos 23:455–473, 2008) of assigning prior probabilities to tree topologies based on the Yule process. By invoking the Principal Principle I argue
that prior probabilities of tree topologies should rather be assigned a weighted mixture of probability distributions based
on Pinelis’ (P Roy Soc Lond B Bio 270:1425–1431, 2003) multi-rate branching process including both the Yule distribution and the uniform distribution. However, I argue that this
solves the problem of the priors of phylogenetic trees only in a weak form. 相似文献
10.
A history of research on arbuscular mycorrhiza 总被引:21,自引:0,他引:21
This is not a review paper in the traditional sense, of which there are many. Three of the most influential reviews that summarized well some of the older literature include those by Nicolson (1967), Gerdemann (1968) and Mosse (1973). Instead, in this brief and incomplete work, we attempt to show the historical development of research on arbuscular mycorrhizas. We owe much to those who have written other historical accounts, including Rayner (1926–1927), Trappe and Berch (1985), Mosse (1985), Schenck (1985), Harley (1991) and Allen (1996), but the contents of this work naturally reflect our own ignorance, interests and biases. It was often difficult to distinguish between the historical and the contemporary, and we did not use any specific cutoff date in making this distinction. The degree to which we include contemporary literature was determined by our own assessment of its connectedness to older literature. In any case, we hope this will be of some interest to those of you who study the arbuscular mycorrhiza, and that it will serve the purpose of providing what we consider to be an important historical context for current researchers. We wish you good fortune in your research.Taken from a paper presented at the COST 8.38 meeting AM Research in Europe (Pisa, Italy): The Dawning of a New Millenium 相似文献
11.
A species is semelparous if every individual reproduces only once in its life and dies immediately after the reproduction.
While the reproduction opportunity is unique per year and the individual’s period from birth to reproduction is just n years, the individuals that reproduce in the ith year (modulo n) are called the ith year class, i = 1, 2, . . . , n. The dynamics of the n year-class system can be described by a differential equation system of Lotka–Volterra type. For the case n = 4, there is a heteroclinic cycle on the boundary as shown in previous works. In this paper, we focus on the case n = 4 and show the existence, growth and disappearance of periodic orbits near the heteroclinic cycle, which is a part of the
conjecture by Diekmann and van Gils (SIAM J Appl Dyn Syst 8:1160–1189, 2009). By analyzing the Poincaré map near the heteroclinic cycle and introducing a metric to measure the size of the periodic
orbit, we show that (i) when the average competitive degree among subpopulations (year classes) in the system is weak, there
exists an asymptotically stable periodic orbit near the heteroclinic cycle which is repelling; (ii) the periodic orbit grows
in size when some competitive degree increases, and converges to the heteroclinic cycle when the average competitive degree
tends to be strong; (iii) when the average competitive degree is strong, there is no periodic orbit near the heteroclinic
cycle which becomes asymptotically stable. Our results provide explanations why periodic solutions expand and disappear and
why all but one subpopulation go extinct. 相似文献
12.
Charles J. Goodnight 《Population Ecology》2005,47(1):3-12
Hamiltons (1964a, 1964b) landmark papers are rightly recognized as the formal basis for our understanding of the evolution of altruistic traits. However, Hamiltons equation as he originally expressed it is simplistic. A genetically oriented approach to studying multilevel selection can provide insights into how the terminology and assumptions used by Hamilton can be generalized. Using contextual analysis I demonstrated that Hamiltons rule actually embodies three distinct processes, group selection, individual selection, and transmission genetics or heritability. Whether an altruistic trait will evolve depends the balance of all of these factors. The genetical approach, and particularly, contextual analysis provides a means of separating these factors and examining them one at a time. Perhaps the greatest issue with Hamiltons equation is the interpretation of r. Hamilton (1964a) interpreted this as relatedness. In this paper I show that what Hamilton called relatedness is more generally interpreted as the proportion for variance among groups, and that many processes in addition to relatedness can increase the variance among groups. I also show that the evolution of an altruistic trait is driven by the ratio of the heritability at the group level to the heritability at the individual level. Under some circumstances this ratio can be greater than 1. In this situation altruism can evolve even if selection favoring selfish behavior is stronger than selection favoring altruism. 相似文献
13.
Marie Doumic-Jauffret Peter S. Kim Benoît Perthame 《Bulletin of mathematical biology》2010,72(7):1732-1759
We analyze the asymptotic behavior of a partial differential equation (PDE) model for hematopoiesis. This PDE model is derived
from the original agent-based model formulated by Roeder (Nat. Med. 12(10):1181–1184, 2006), and it describes the progression of blood cell development from the stem cell to the terminally differentiated state. 相似文献
14.
Kazunori Sato 《Population Ecology》2009,51(3):411-418
In this paper, we investigate a spatially explicit metapopulation model with Allee effects. We refer to the patch occupancy
model introduced by Levins (Bull Entomol Soc Am 15:237–240, 1969) as a spatially implicit metapopulation model, i.e., each local patch is either occupied or vacant and a vacant patch can
be recolonized by a randomly chosen occupied patch from anywhere in the metapopulation. When we transform the model into a
spatially explicit one by using a lattice model, the obtained model becomes theoretically equivalent to a “lattice logistic
model” or a “basic contact process”. One of the most popular or standard metapopulation models with Allee effects, developed
by Amarasekare (Am Nat 152:298–302, 1998), supposes that those effects are introduced formally by means of a logistic equation. However, it is easier to understand
the ecological meaning of associating Allee effects with this model if we suppose that only the logistic colonization term
directly suffers from Allee effects. The resulting model is also well defined, and therefore we can naturally examine it by
Monte Carlo simulation and by doublet and triplet decoupling approximation. We then obtain the following specific features
of one-dimensional lattice space: (1) the metapopulation as a whole does not have an Allee threshold for initial population
size even when each local population follows the Allee effects; and (2) a metapopulation goes extinct when the extinction
rate of a local population is lower than that in the spatially implicit model. The real ecological metapopulation lies between
two extremes: completely mixing interactions between patches on the one hand and, on the other, nearest neighboring interactions
with only two nearest neighbors. Thus, it is important to identify the metapopulation structure when we consider the problems
of invasion species such as establishment or the speed of expansion. 相似文献
15.
Clara Stefen 《Pal?ontologische Zeitschrift》2009,83(1):183-186
The Early/Middle Miocene boundary locality Sandelzhausen (MN5, southern Germany) yielded three beaver teeth: one lower incisor
fragment and two strongly worn upper premolars, a right and a left one. The latter are so similar in wear, height, size, and
enamel pattern that they probably represent one individual. Although the teeth have been referred to Chalicomys jaegeri Kaup, 1832 (e.g., Hugueney 1999, Fahlbusch 2003), it seems more likely that they belong to Steneofiber depereti Mayet, 1908. However, the assignment of the present material to either one of these species is difficult, because in the advanced wear
stage some diagnostic characteristics cannot be assessed. As to ecological implications for the locality Sandelzhausen the
taxonomic identity of these two beaver species may not be important. Both are known from riverine, lacustrine or swamp sediments,
and it can be assumed that they usually lived in close vicinity to water. Thus, the presence of beaver remains supports the
presence of water at Sandelzhausen. However, the teeth might have an allochthonous origin from creeks of the rising Alps.
相似文献
16.
Pierre Mein 《Pal?ontologische Zeitschrift》2009,83(1):141-150
In this note the taxonomic position of the tiny eomyid genus Keramidomys (Hartenberger, 1967) from the Early/Middle Miocene boundary locality of Sandelzhausen in the Bavarian Upper Freshwater Molasse is reexamined.
As the chronological dating of the Sandelzhausen fossil site has been modified in the past from formerly the Neogene mammal
unit MN6 to now MN5 and thanks to new abundant material this rodent is compared with other European forms. It is shown that
the Sandelzhausen eomyid must be called K. thaleri Hugueney & Mein, 1968 on the basis of several morphological dental differences from K. carpathicus Schaub & Zapfe, 1953. This rodent seems to be an immigrant from East Asia into Europe. Even if K. thaleri is known in many European localities, all correlated to MN5, it is always a rare element of European rodent faunas. Differentiation
from K. carpathicus is not easy and requires a sufficiently large sample.
相似文献
17.
Yasuhiro Fukushima Minoru Tsukada Ichiro Tsuda Yutaka Yamaguti Shigeru Kuroda 《Cognitive neurodynamics》2007,1(4):305-316
To clarify how the information of spatiotemporal sequence of the hippocampal CA3 affects the postsynaptic membrane potentials
of single pyramidal cells in the hippocampal CA1, the spatio-temporal stimuli was delivered to Schaffer collaterals of the
CA3 through a pair of electrodes and the post-synaptic membrane potentials were recorded using the patch-clamp recording method.
The input–output relations were sequentially analyzed by applying two measures; “spatial clustering” and its “self-similarity”
index. The membrane potentials were hierarchically clustered in a self-similar manner to the input sequences. The property
was significantly observed at two and three time-history steps. In addition, the properties were maintained under two different
stimulus conditions, weak and strong current stimulation. The experimental results are discussed in relation to theoretical
results of Cantor coding, reported by Tsuda (Behav Brain Sci 24(5):793–847, 2001) and Tsuda and Kuroda (Jpn J Indust Appl Math 18:249–258, 2001; Cortical dynamics, pp 129–139, Springer-Verlag, 2004). 相似文献
18.
Grote MJ Palumberi V Wagner B Barbero A Martin I 《Journal of mathematical biology》2011,63(4):757-777
Growth factors have a significant impact not only on the growth dynamics but also on the phenotype of chondrocytes (Barbero
et al. in J. Cell. Phys. 204:830–838, 2005). In particular, as chondrocytes approach confluence, the cells tend to align and form coherent patches. Starting from a
mathematical model for fibroblast populations at equilibrium (Mogilner et al. in Physica D 89:346–367, 1996), a dynamic continuum model with logistic growth is developed. Both linear stability analysis and numerical solutions of
the time-dependent nonlinear integro-partial differential equation are used to identify the key parameters that lead to pattern
formation in the model. The numerical results are compared quantitatively to experimental data by extracting statistical information
on orientation, density and patch size through Gabor filters. 相似文献
19.
It was shown in a previous study by Stålhand et al. (2004) that both material and residual strain parameters for an artery can be identified noninvasively from an in vivo clinical pressure–diameter measurement. The only constraints placed on the model parameters in this previous study was a set of simple box constraints. More advanced constraints can also be utilized, however. These constraints restrict the model parameters implicitly by demanding the state of the artery to behave in a specified way. It has been observed in vitro that the axial force is nearly invariant to the pressure at the physiological operation point. In this paper, we study the possibility to include this behaviour as a constraint in the parameter optimization. The method is tested on an in vivo obtained pressure–diameter cycle for a 24-year-old human. Presented results show that the constrained parameter identification procedure proposed here can be used to obtain good results, and we believe that it may be applied to account for other observed behaviours as well. 相似文献
20.
Agarwal B 《Journal of bioenergetics and biomembranes》2011,43(3):299-310
ATP, the ‘universal biological energy currency’, is synthesized by utilizing energy either from oxidation of fuels or from
light, via the process of oxidative and photo-phosphorylation respectively. The process is mediated by the enzyme F1F0-ATP synthase, using the free energy of ion gradients in the final energy catalyzing step, i.e., the synthesis of ATP from
ADP and inorganic phosphate (Pi). The details of the molecular mechanism of ATP synthesis are among the most important fundamental issues in biology and
hence need to be properly understood. In this work, a role for anions in making ATP has been found. New experimental data
has been reported on the inhibition of ATP synthesis at nanomolar concentrations by the potent, specific anion channel blockers
4,4′-diisothiocyanostilbene-2, 2′-disulphonic acid (DIDS) and tributyltin chloride (TBTCl). Based on these inhibition studies,
attention has been drawn to anion translocation (in addition to proton translocation) as a requirement for ATP synthesis.
The type of inhibition has been quantified and an overall kinetic scheme for mixed inhibition that explains the data has been
evolved. The experimental data and the type of inhibition found have been interpreted in the light of the torsional mechanism
of energy transduction and ATP synthesis (Nath J Bioenerg Biomembr 42:293–300, 2010a; J Bioenerg Biomembr 42:301–309, 2010b). This detailed and unified mechanism resolves long-standing problems and inconsistencies in the first theories (Slater Nature
172:975–978, 1953; Williams J Theor Biol 1:1–17, 1961; Mitchell Nature 191:144–148, 1961; Mitchell Biol Rev 41:445–502, 1966), makes several novel predictions that are experimentally verifiable (Nath Biophys J 90:8–21, 2006a; Process Biochem 41:2218–2235, 2006b), and provides us with a new and fruitful paradigm in bioenergetics. The interpretation presented here provides intelligent
answers to the unexplained existing results in the literature. It is shown that mechanistic interpretation of the experimental
data requires substantial addition to available conceptual foundations such that present concepts, theories, and mechanisms
must be revised. 相似文献