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Florian M. Steiner Wolfgang Arthofer Birgit C. Schlick-Steiner Ross H. Crozier Christian Stauffer 《Conservation Genetics》2008,9(3):757-759
Invasive species trigger biodiversity losses and alter ecosystem functioning, with life history shaping invasiveness (Sakai
et al., Annu Rev Ecol Syst 32:305–332, 2001). However, pinpointing the relation of a specific life history to invasion success
is difficult. One approach may be comparing congeners. The two Palearctic pavement ants, Tetramorium sp.E (widely known as T. caespitum, Schlick-Steiner et al., Mol Phylogenet Evol 40:259–273, 2006) and T. tsushimae have invaded North America (Steiner et al., Biol Invasions 8:117–123, 2006). Their life histories differ in that T. sp.E has separate single-queened colonies but T. tsushimae multi-queened colonies scattered over large areas (Sanada-Morimura et al., Insect Soc 53:141–148, 2006; Schlick-Steiner et al.,
Mol Phylogenet Evol 40:259–273, 2006; Steiner et al., Biol Invasions 8:117–123, 2006). Comparison of the genetic diversity in the entire native and non-native ranges will elucidate the invasion histories. Here,
we present 13 and 11 microsatellites, developed for T. sp.E and T. tsushimae, respectively, and characterize all for both species.
Florian M. Steiner, Wolfgang Arthofer and Birgit C. Schlick-Steiner contributed equally to this work. 相似文献
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In plants, reactive oxygen species (ROS) are short-lived molecules produced through various cellular mechanisms in response
to biotic and abiotic stimuli. ROS function as second messengers for hormone signaling, development, oxygen deprivation, programmed
cell death, and plant–pathogen interactions. Recent research on ROS-mediated responses has produced stimulating findings such
as the specific sources of ROS production, molecular elements that work in ROS-mediated signaling and homeostasis, and a ROS-regulated
gene network (Neill et al., Curr Opin Plant Biol 5:388–395, 2002a; Apel and Hirt, Annu Rev Plant Biol 55:373–399, 2004; Mittler et al., Trends Plant Sci 9:490–498, 2004; Mori and Schroeder, Plant Physiol 135:702–708, 2004; Kwak et al., Plant Physiol 141:323–329, 2006; Torres et al., Plant Physiol 141:373–378, 2006; Miller et al., Physiol Plant 133:481–489, 2008). In this review, we highlight new discoveries in ROS-mediated abscisic acid (ABA) signaling.
Drs. Daeshik Cho and June M. Kwak are the corresponding authors for this paper. 相似文献
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Andrei S. Rodin Sergei N. Rodin Charles W. CarterJr. 《Journal of molecular evolution》2009,69(5):555-567
The genetic code is implemented by aminoacyl-tRNA synthetases (aaRS). These 20 enzymes are divided into two classes that,
despite performing same functions, have nothing common in structure. The mystery of this striking partition of aaRSs might
have been concealed in their sterically complementary modes of tRNA recognition that, as we have found recently, protect the
tRNAs with complementary anticodons from confusion in translation. This finding implies that, in the beginning, life increased
its coding repertoire by the pairs of complementary codons (rather than one-by-one) and used both complementary strands of
genes as templates for translation. The class I and class II aaRSs may represent one of the most important examples of such
primordial sense–antisense (SAS) coding (Rodin and Ohno, Orig Life Evol Biosph 25:565–589, 1995). In this report, we address the issue of SAS coding in a wider scope. We suggest a variety of advantages that such coding
would have had in exploring a wider sequence space before translation became highly specific. In particular, we confirm that
in Achlya klebsiana a single gene might have originally coded for an HSP70 chaperonin (class II aaRS homolog) and an NAD-specific GDH-like enzyme
(class I aaRS homolog) via its sense and antisense strands. Thus, in contrast to the conclusions in Williams et al. (Mol Biol
Evol 26:445–450, 2009), this could indeed be a “Rosetta stone” gene (Carter and Duax, Mol Cell 10:705–708, 2002) (eroded somewhat, though) for the SAS origin of the two aaRS classes. 相似文献
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Zachary Cooper Michael Greenwood Borbala Mazzag 《Bulletin of mathematical biology》2009,71(7):1543-1579
We investigate the role of heterogeneous expression of IP3R and RyR in generating diverse elementary Ca2+ signals. It has been shown empirically (Wojcikiewicz and Luo in Mol. Pharmacol. 53(4):656–662, 1998; Newton et al. in J. Biol. Chem. 269(46):28613–28619, 1994; Smedt et al. in Biochem. J. 322(Pt. 2):575–583, 1997) that tissues express various proportions of IP3 and RyR isoforms and this expression is dynamically regulated (Parrington et al. in Dev. Biol. 203(2):451–461, 1998; Fissore et al. in Biol. Reprod. 60(1):49–57, 1999; Tovey et al. in J. Cell Sci. 114(Pt. 22):3979–3989, 2001). Although many previous theoretical studies have investigated the dynamics of localized calcium release sites (Swillens
et al. in Proc. Natl. Acad. Sci. U.S.A. 96(24):13750–13755, 1999; Shuai and Jung in Proc. Natl. Acad. Sci. U.S.A. 100(2):506–510, 2003a; Shuai and Jung in Phys. Rev. E, Stat. Nonlinear Soft Matter Phys. 67(3 Pt. 1):031905, 2003b; Thul and Falcke in Biophys. J. 86(5):2660–2673, 2004; DeRemigio and Smith in Cell Calcium 38(2):73–86, 2005; Nguyen et al. in Bull. Math. Biol. 67(3):393–432, 2005), so far all such studies focused on release sites consisting of identical channel types. We have extended an existing mathematical
model (Nguyen et al. in Bull. Math. Biol. 67(3):393–432, 2005) to release sites with two (or more) receptor types, each with its distinct channel kinetics. Mathematically, the release
site is represented by a transition probability matrix for a collection of nonidentical stochastically gating channels coupled
through a shared Ca2+ domain. We demonstrate that under certain conditions a previously defined mean-field approximation of the coupling strength
does not accurately reproduce the release site dynamics. We develop a novel approximation and establish that its performance
in these instances is superior. We use this mathematical framework to study the effect of heterogeneity in the Ca2+-regulation of two colocalized channel types on the release site dynamics. We consider release sites consisting of channels
with both Ca2+-activation and inactivation (“four-state channels”) and channels with Ca2+-activation only (“two-state channels”) and show that for the appropriate parameter values, synchronous channel openings within
a release site with any proportion of two-state to four-state channels are possible, however, the larger the proportion of
two-state channels, the more sensitive the dynamics are to the exact spatial positioning of the channels and the distance
between channels. Specifically, the clustering of even a small number of two-state channels interferes with puff/spark termination
and increases puff durations or leads to a tonic response. 相似文献
9.
The Protein Kinase C family of enzymes is a group of serine/threonine kinases that play central roles in cell-cycle regulation,
development and cancer. A key step in the activation of PKC is translocation to membranes and binding of membrane-associated
activators including diacylglycerol (DAG). Interaction of novel and conventional isotypes of PKC with DAG and phorbol esters
occurs through the two C1 regulatory domains (C1A and C1B), which exhibit distinct ligand binding selectivity that likely
controls enzyme activation by different co-activators. PKC has also been implicated in physiological responses to alcohol
consumption and it has been proposed that PKCα (Slater et al. J Biol Chem 272(10):6167–6173, 1997; Slater et al. Biochemistry 43(23):7601–7609, 2004), PKCε (Das et al. Biochem J 421(3):405–413, 2009) and PKCδ (Das et al. J Biol Chem 279(36):37964–37972, 2004; Das et al. Protein Sci 15(9):2107–2119, 2006) contain specific alcohol-binding sites in their C1 domains. We are interested in understanding how ethanol affects signal
transduction processes through its affects on the structure and function of the C1 domains of PKC. Here we present the 1H, 15N and 13C NMR chemical shift assignments for the Rattus norvegicus PKCδ C1A and C1B proteins. 相似文献
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The problem of how often to disperse in a randomly fluctuating environment has long been investigated, primarily using patch
models with uniform dispersal. Here, we consider the problem of choice of seed size for plants in a stable environment when
there is a trade off between survivability and dispersal range. Ezoe (J Theor Biol 190:287–293, 1998) and Levin and Muller-Landau (Evol Ecol Res 2:409–435, 2000) approached this problem using models that were essentially deterministic, and used calculus to find optimal dispersal parameters.
Here we follow Hiebeler (Theor Pop Biol 66:205–218, 2004) and use a stochastic spatial model to study the competition of different dispersal strategies. Most work on such systems
is done by simulation or nonrigorous methods such as pair approximation. Here, we use machinery developed by Cox et al. (Voter
model perturbations and reaction diffusion equations 2011) to rigorously and explicitly compute evolutionarily stable strategies. 相似文献
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Mol. Biol. Evol. 25:120–130. 2008. doi:10.1093/molbev/msm248 Numerical values in 相似文献
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Siderophore production by marine-derived fungi 总被引:1,自引:0,他引:1
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Estimation of evolutionary distances between nucleotide sequences 总被引:11,自引:0,他引:11
Andrey Zharkikh 《Journal of molecular evolution》1994,39(3):315-329
A formal mathematical analysis of the substitution process in nucleotide sequence evolution was done in terms of the Markov process. By using matrix algebra theory, the theoretical foundation of Barry and Hartigan's (Stat. Sci. 2:191–210, 1987) and Lanave et al.'s (J. Mol. Evol. 20:86–93, 1984) methods was provided. Extensive computer simulation was used to compare the accuracy and effectiveness of various methods for estimating the evolutionary distance between two nucleotide sequences. It was shown that the multiparameter methods of Lanave et al.'s (J. Mol. Evol. 20:86–93, 1984), Gojobori et al.'s (J. Mol. Evol. 18:414–422, 1982), and Barry and Hartigan's (Stat. Sci. 2:191–210, 1987) are preferable to others for the purpose of phylogenetic analysis when the sequences are long. However, when sequences are short and the evolutionary distance is large, Tajima and Nei's (Mol. Biol. Evol. 1:269–285, 1984) method is superior to others. 相似文献
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Somites are condensations of mesodermal cells that form along the two sides of the neural tube during early vertebrate development.
They are one of the first instances of a periodic pattern, and give rise to repeated structures such as the vertebrae. A number
of theories for the mechanisms underpinning somite formation have been proposed. For example, in the “clock and wavefront”
model (Cooke and Zeeman in J. Theor. Biol. 58:455–476, 1976), a cellular oscillator coupled to a determination wave progressing along the anterior-posterior axis serves to group cells
into a presumptive somite. More recently, a chemical signaling model has been developed and analyzed by Maini and coworkers
(Collier et al. in J. Theor. Biol. 207:305–316, 2000; Schnell et al. in C. R. Biol. 325:179–189, 2002; McInerney et al. in Math. Med. Biol. 21:85–113, 2004), with equations for two chemical regulators with entrained dynamics. One of the chemicals is identified as a somitic factor,
which is assumed to translate into a pattern of cellular aggregations via its effect on cell–cell adhesion. Here, the authors
propose an extension to this model that includes an explicit equation for an adhesive cell population. They represent cell
adhesion via an integral over the sensing region of the cell, based on a model developed previously for adhesion driven cell
sorting (Armstrong et al. in J. Theor. Biol. 243:98–113, 2006). The expanded model is able to reproduce the observed pattern of cellular aggregates, but only under certain parameter restrictions.
This provides a fuller understanding of the conditions required for the chemical model to be applicable. Moreover, a further
extension of the model to include separate subpopulations of cells is able to reproduce the observed differentiation of the
somite into separate anterior and posterior halves.
N.J. Armstrong was supported by a Doctoral Training Account Studentship from EPSRC. K.J. Painter and J.A. Sherratt were supported
in part by Integrative Cancer Biology Program Grant CA113004 from the US National Institute of Health and in part by BBSRC
grant BB/D019621/1 for the Centre for Systems Biology at Edinburgh. 相似文献
15.
F. Ann Walker 《Journal of biological inorganic chemistry》2006,11(4):391-397
The 1H NMR chemical shifts of the heme methyl groups of the ferriheme complex of metneuroglobin (Du et al. in J. Am. Chem. Soc. 125:8080–8081, 2003) predict orientations of the axial histidine ligands (Shokhirev and Walker in J. Biol. Inorg. Chem. 3:581–594, 1998) that are not consistent with the X-ray data (Vallone et al. in Proteins Struct. Funct. Bioinf. 56:85–94, 2004), and the EPR spectrum (Vinck et al. in J. Am. Chem. Soc. 126:4516–4517, 2004) is only marginally consistent with these data. The reasons for these inconsistencies appear to be rooted in the high degree of aqueous solution exposure of the heme group and the fact that there are no strong hydrogen-bond acceptors for the histidine imidazole N–H protons provided by the protein. Similar inconsistencies may exist for other water-soluble heme proteins, and 1H NMR spectroscopy provides a simple means to verify whether the solution structure of the heme center is the same as or different from that in the crystalline state. 相似文献
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Yeang Chen-Hsiang; Darot Jeremy F. J.; Noller Harry F.; Haussler David 《Molecular biology and evolution》2007,24(10):2354
Mol. Biol. Evol. 24: 1592–1595. 2007. doi:10.1093/molbev/msm142 The following corrections were not incorporated into the paper: 1) In 相似文献
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Xiangjiang Zhan Xiudeng Zheng Michael W. Bruford Fuwen Wei Yi Tao 《Conservation Genetics》2010,11(4):1567-1571
More and more noninvasive genetic data are being produced but a general methodology to quantify genotyping error rates from
non-pilot data remains lacking. Here we propose a mathematical approach to estimate genotyping error rates by exploring the
relationship between errors and PCR replicates. This method can be used to quantify the error rates for either the multi-tubes
approach designed by Taberlet et al. (Nucleic Acids Res 24: 3189–3194, 1996) or the pilot method by Prugh et al. (Mol Ecol 14: 1585–1596, 2005). 相似文献
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Genka H Baba T Tsuda M Kanaya S Mori H Yoshida T Noguchi MT Tsuchiya K Sawada H 《Journal of molecular evolution》2006,63(3):401-414
DNA fragments containing argK-tox clusters and their flanking regions were cloned from the chromosomes of Pseudomonas syringae pathovar (pv.) actinidiae strain KW-11 (ACT) and P. syringae pv. phaseolicola strain MAFF 302282 (PHA), and then their sequences were determined. Comparative analysis of these sequences and the sequences
of P. syringae pv. tomato DC3000 (TOM) (Buell et al., Proc Natl Acad Sci USA 100:10181–10186, 2003) and pv. syringae B728a (SYR) (Feil et al., Proc Natl Acad Sci USA 102:11064–11069, 2005) revealed that the chromosomal backbone regions of ACT and TOM shared a high similarity to each other but presented a low
similarity to those of PHA and SYR. Nevertheless, almost-identical DNA regions of about 38 kb were confirmed to be present
on the chromosomes of both ACT and PHA, which we named “tox islands.” The facts that the GC content of such tox islands was 6% lower than that of the chromosomal backbone regions of P. syringae, and that argK-tox clusters, which are considered to be of exogenous origin based on our previous studies (Sawada et al., J Mol Evol 54:437–457,
2002), were confirmed to be contained within the tox islands, suggested that the tox islands were an exogenous, mobile genetic element inserted into the chromosomes of P. syringae strains. It was also predicted that the tox islands integrated site-specifically into the homologous sites of the chromosomes of ACT and PHA in the same direction, respectively,
wherein 34 common gene coding sequences (CDSs) existed. Furthermore, at the left end of the tox islands were three CDSs, which encoded polypeptides and had similarities to the members of the tyrosine recombinase family,
suggesting that these putative site-specific recombinases were involved in the recent horizontal transfer of tox islands.
Electronic Supplementary Material Electronic Supplementary material is available for this article at
and accessible for authorised users. 相似文献
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John T. Salvucci 《Cell and tissue banking》2011,12(2):99-104
Over the past 57 years, 17 recipients of frozen bone have been infected with: HIV (Centers for Disease Control and Prevention
in Morb Mortal Wkly Rep MMWR 37(39):597–599, 1988; Li et al. in J Formos Med Assoc 100(5):350–351, 2001; Simonds et al. in NEJM 326(11):726–732, 1992; Schratt et al. in Unfallchirurg 99(9):679–684, 1996); HCV (Eggen and Nordbo in NEJM 326(6):411, 1992; Conrad et al. in J Bone Joint Surg Am 77:214–224, 1995; Trotter in J Bone Joint Surg Am 851(11):2215–2217, 2003; Tugwell et al. in Ann of Internal Med 143(9):648–654, 2005); or HBV (Shutkin in J Bone Joint Surg Am 36:160–162, 1954). However, bone, lyophilized and stored at room temperature, has never transmitted these viral diseases. A literature review
was undertaken to determine whether there is any evidence that lyophilized bone is capable of transmitting HIV, HCV and HBV. 相似文献