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1.
Comparison of the crystal structures of the KcsA and MthK potassium channels suggests that the process of opening a K+ channel involves pivoted bending of the inner pore-lining helices at a highly conserved glycine residue. This bending motion
is proposed to splay the transmembrane domains outwards to widen the gate at the “helix-bundle crossing”. However, in the
inwardly rectifying (Kir) potassium channel family, the role of this “hinge” residue in the second transmembrane domain (TM2)
and that of another putative glycine gating hinge at the base of TM2 remain controversial. We investigated the role of these
two positions in heteromeric Kir4.1/Kir5.1 channels, which are unique amongst Kir channels in that both subunits lack a conserved
glycine at the upper hinge position. Contrary to the effect seen in other channels, increasing the potential flexibility of
TM2 by glycine substitutions at the upper hinge position decreases channel opening. Furthermore, the contribution of the Kir4.1
subunit to this process is dominant compared to Kir5.1, demonstrating a non-equivalent contribution of these two subunits
to the gating process. A homology model of heteromeric Kir4.1/Kir5.1 shows that these upper “hinge” residues are in close
contact with the base of the pore α-helix that supports the selectivity filter. Our results also indicate that the highly
conserved glycine at the “lower” gating hinge position is required for tight packing of the TM2 helices at the helix-bundle
crossing, rather than acting as a hinge residue. 相似文献
2.
GluR0 is a prokaryotic homologue of mammalian glutamate receptors that forms glutamate-activated, potassium-selective ion channels. The topology of its transmembrane (TM) domain is similar to that of simple potassium channels such as KcsA. Two plausible alignments of the sequence of the TM domain of GluR0 with KcsA are possible, differing in the region of the P helix. We have constructed homology models based on both alignments and evaluated them using 6 ns duration molecular dynamics simulations in a membrane-mimetic environment. One model, in which an insertion in GluR0 relative to KcsA is located in the loop between the M1 and P helices, is preferred on the basis of lower structural drift and maintenance of the P helix conformation during simulation. This model also exhibits inter-subunit salt bridges that help to stabilise the TM domain tetramer. During the simulation, concerted K(+) ion-water movement along the selectivity filter is observed, as is the case in simulations of KcsA. K(+) ion exit from the central cavity is associated with opening of the hydrophobic gate formed by the C-termini of the M2 helices. In the intact receptor the opening of this gate will be controlled by interactions with the extramembranous ligand-binding domains. 相似文献
3.
Michael Stoehr Alvin Yanchuk Chang-Yi Xie Leopoldo Sanchez 《Tree Genetics & Genomes》2008,4(2):193-200
Sublines are used in the third-generation breeding and testing of coastal Douglas-fir in British Columbia, with the original
intent of selecting only one genotype per subline for production populations (e.g., seed orchards) to eliminate relatedness
among parents (therein called “1/SL”). We evaluated three additional selection scenarios that did not consider the subline
structure. One of the scenarios strictly selected on the basis of the highest breeding values of the trees (“TOP”); another
scenario used the TOP selections, but assigned the number of ramets per selection proportionally to the selection breeding
value (“LIND”); lastly, a simulated annealing technique was applied to maximize gain under explicit constraints on coancestry
(“OPTS”). All three alternative selection scenarios resulted in some relatedness and coancestry among selections, but the
last two provided increases in average breeding values compared to those obtained by the 1/SL scenario. Effective population
sizes (and consequently inbreeding coefficients) varied among the three selection scenarios. Effects of the various selections
on merchantable volume at rotation age were determined using a linear regression model based on an individual tree model (TASS),
which was first run to determine the relationship between merchantable volume and inbreeding (f). LIND and TOP selections yielded the highest breeding values but, due to the increased coancestry among selections, paid
a penalty in the merchantable volume determination. OPTS maximized merchantable volume at rotation age 60 after including
more than 13 selections with an increase of around 3% over that obtained by the 1/SL selection scenario, with an associated
increase in Ne of 50%. Other implications of the three alternative selection scenarios are discussed. 相似文献
4.
P. Slurink 《Human Evolution》1993,8(4):265-273
In contrast to many other models of human evolution the “balance of power” theory of Alexander has a clear answer to the question
why a runaway selection process for unique social and moral capacities occurred in our ancestry only and not in other species:
“ecological dominance” is hypothesized to have diminished the effects of “extrinsic” forces of natural selection such that
withinspecies, intergroup competition increased (Alexander, 1989). Alexander seems to be wrong, however, in his claim that
already the common HUCHIBO (Humans, Chimps, Bonobo's)-ancestor has crossed the ecological dominance barrier. In this paper
an adapted version of Alexander's model is presented and several different ways are proposed to make this adapted version
testable. A preliminary survey of the available paleontological and paleoecological data suggests that there is some evidence
of a less vulnerable position towards predators in earlyHomo and that there are clear signs related to a crossing of the ecological dominance barrier inHomo sapiens sapiens. 相似文献
5.
W. A. Yuhas P. A. Fuchs 《Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology》1999,185(5):455-462
Acetylcholine released from efferent neurons in the cochlea causes inhibition of mechanosensory hair cells due to the activation
of calcium-dependent potassium channels. Hair cells are known to have large-conductance, “BK”-type potassium channels associated
with the afferent synapse, but these channels have different properties than those activated by acetylcholine. Whole-cell (tight-seal) and
cell-attached patch-clamp recordings were made from short (outer) hair cells isolated from the chicken basilar papilla (cochlea
equivalent). The peptides apamin and charybdotoxin were used to distinguish the calcium-activated potassium channels involved
in the acetylcholine response from the BK-type channels associated with the afferent synapse. Differential toxin blockade
of these potassium currents provides definitive evidence that ACh activates apamin-sensitive, “SK”-type potassium channels,
but does not activate carybdotoxin-sensitive BK channels. This conclusion is supported by tentative identification of small-conductance,
calcium-sensitive but voltage-insensitive potassium channels in cell-attached patches. The distinction between these channel
types is important for understanding the segregation of opposing afferent and efferent synaptic activity in the hair cell,
both of which depend on calcium influx. These different calcium-activated potassium channels serve as sensitive indicators
for functionally significant calcium influx in the hair cell.
Accepted: 12 August 1999 相似文献
6.
The CD59-coding sequences were obtained from 5 mammals by PCR and BLAST, and combined with the available sequences in GenBank,
the nucleotide substitution rates of mammalian cd59 were calculated. Results of synonymous and nonsynonymous substitution rates revealed that cd59 experienced negative selection in mammals overall. Four sites experiencing positive selection were found by using “site-specific”
model in PAML software. These sites were distributed on the molecular surface, of which 2 sites located in the key functional
domain. Furthermore, “branch-site-specific” model detected 1 positive site in cd59a and cd59b lineages which underwent accelerated evolution caused by positive selection after gene duplication in mouse. 相似文献
7.
Electrostatic potentials created by fixed or induced charges regulate many cellular phenomena including the rate of ion transport
through proteinaceous ion channels. Nanometer-scale pores of these channels also play a critical role in the transport of
charged and neutral macromolecules. We demonstrate here that, surprisingly, changing the charge state of a channel markedly
alters the ability of nonelectrolyte polymers to enter the channel's pore. Specifically, we show that the partitioning of differently-sized linear nonelectrolyte
polymers of ethylene glycol into the Staphylococcus aureus α-hemolysin channel is altered by the solution pH. Protonating some of the channel side chains decreases the characteristic
polymer size (molecular weight) that can enter the pore by ∼25% but increases the ionic current by ∼15%. Thus, the “steric”
and “electric” size of the channel change in opposite directions. The results suggest that effects due to polymer and channel
hydration are crucial for polymer transport through such pores.
Received: 16 March 1997 / Accepted: 24 April 1997 相似文献
8.
“Candidatus Liberobacter,” the uncultured bacterium associated with citrus Huanglongbing (HLB) disease, is an α-Proteobacteria, and two species, “Candidatus L. africanum” and “Candidatus L. asiaticum,” have been characterized by sequence analysis of the 16S rDNA and β operon (rplKAJL-rpoBC) genes. These genes were isolated by PCR and random cloning of DNA from infected plants. However, this strategy is laborious
and allowed selection of only three Liberobacter DNA fragments. In this paper, we described isolation of additional genes
using Random Amplified Polymorphic DNA (RAPD). In total, 102 random 10-mer primers were used in PCR reactions on healthy and
Liberobacter-infected plant DNA. Eight DNA bands amplified from infected plant DNA were cloned and analyzed. Six of them were
found to be part of the Liberobacter genome by sequence and hybridization experiments. On these DNA fragments, four genes
were identified: nusG, pgm, omp, and a hypothetical protein gene. These results indicate that RAPD can be used to clone DNA of uncultured organisms.
Received: 14 September 1998 / Accepted: 6 October 1998 相似文献
9.
An important criterion used to detect adaptive evolution in DNA sequence data is ωi > 1, where ωi is the ratio of nonsynonymous to synonymous substitution rates in lineage i. However, the evaluation of multiple ωi within a phylogenetic tree can easily inflate the statistical type I error rate. We developed two rigorous methods of analysis
that avoid this and other potential pitfalls. We applied these methods to four published examples of adaptive evolution. One
case was strongly supported by our reanalysis (abalone sperm lysin), and one was weakly supported (baboon α-globin), but two
examples (primate lysozyme and Antarctic fish β-globin) did not show significant evidence of adaptive evolution. Our first
method is a “bottom-up” hierarchical maximum likelihood approach, which (1) tests for significant heterogeneity in ω across
the phylogeny, (2) locates its source using a sequence of planned comparisons, and (3) tests homogeneous groups of ω for ω
> 1, using a modified level of significance that incorporates the pretesting. The second method is a “top-down” log-linear
analysis based on estimates of nonsynonymous and synonymous substitutions in pairs of lineages. The log-linear test is applied
to pairs of lineages joined at progressively deeper nodes. For each pair, the analysis simultaneously tests for adaptive evolution
(ω > 1), a shift in natural selection (ω1 ≠ω2), and unequal evolution rate (the relative rate test). In both tests, we emphasized that the criterion ω1 ≠ ω2 is an important additional indicator of a phylogenetic shift in the balance between natural selection and genetic drift between
two related lineages.
[Reviewing Editor: Dr. John Huelsenbeck] 相似文献
10.
Evolutionary biology owes much to Charles Darwin, whose discussions of common descent and natural selection provide the foundations
of the discipline. But evolutionary biology has expanded well beyond its foundations to encompass many theories and concepts
unknown in the 19th century. The term “Darwinism” is, therefore, ambiguous and misleading. Compounding the problem of “Darwinism”
is the hijacking of the term by creationists to portray evolution as a dangerous ideology—an “ism”—that has no place in the
science classroom. When scientists and teachers use “Darwinism” as synonymous with evolutionary biology, it reinforces such
a misleading portrayal and hinders efforts to present the scientific standing of evolution accurately. Accordingly, the term
“Darwinism” should be abandoned as a synonym for evolutionary biology. 相似文献
11.
Christian Reidys Peter F. Stadler Peter Schuster 《Bulletin of mathematical biology》1997,59(2):339-397
Random graph theory is used to model and analyse the relationship between sequences and secondary structures of RNA molecules,
which are understood as mappings from sequence space into shape space. These maps are non-invertible since there are always
many orders of magnitude more sequences than structures. Sequences folding into identical structures formneutral networks. A neutral network is embedded in the set of sequences that arecompatible with the given structure. Networks are modeled as graphs and constructed by random choice of vertices from the space of compatible
sequences. The theory characterizes neutral networks by the mean fraction of neutral neighbors (λ). The networks are connected
and percolate sequence space if the fraction of neutral nearest neighbors exceeds a threshold value (λ>λ*). Below threshold
(λ<λ*), the networks are partitioned into a largest “giant” component and several smaller components. Structure are classified
as “common” or “rare” according to the sizes of their pre-images, i.e. according to the fractions of sequences folding into
them. The neutral networks of any pair of two different common structures almost touch each other, and, as expressed by the
conjecture ofshape space covering sequences folding into almost all common structures, can be found in a small ball of an arbitrary location in sequence space.
The results from random graph theory are compared to data obtained by folding large samples of RNA sequences. Differences
are explained in terms of specific features of RNA molecular structures.
Deicated to professor Manfred Eigen 相似文献
12.
Dynamic role of “illite-like” clay minerals in temperate soils: facts and hypotheses 总被引:2,自引:0,他引:2
Analysis of new data and reinterpretation of published information for clay minerals found in temperate climate soil profiles
indicates that there is often a gradient of “illite-like” clay minerals with depth. We used the term “illite-like” because
these observations are based on X-Ray Diffractogram patterns and not on layer charge measurements which allow to define properly
illite. It appears that “illite-like” layers are concentrated in the upper, organic - rich portion of the soil profile both
under grassland and forest vegetation. “Illite-like” layer quantity seems directly related to soil potassium status. Indeed,
intensive agriculture practises without potassium fertilization reduce “illite-like” content in surface soils, whereas several
years of potassic fertilization without plant growth can increase “illite-like” content. The potassic soil clay mineral, illite,
is particularly important in that it can be the major source of readily available potassium for plants. Spatial and temporal
dynamics of clay minerals should be related to the potassium cycle. We propose that the frequently observed general trend
of increasing exchangeable potassium in the top soil can be correlated with an increase in “illite-like” in the clays and
that the decrease of potassium caused by intensive agricultural practices leads to “illite-like” layer destabilization. This
vision of “illite-like” layer as a potassium reservoir refueled by plants and emptied by intensive cropping renews the concept
of potassium availability and indicates a need to be discussed as well in natural ecosystems as in cultivated ecosystems. 相似文献
13.
This article deals with the relationship between vocabulary (total number of distinct oligomers or “words”) and text-length
(total number of oligomers or “words”) for a coding DNA sequence (CDS). For natural human languages, Heaps established a mathematical
formula known as Heaps' law, which relates vocabulary to text-length. Our analysis shows that Heaps' law fails to model this
relationship for CDSs. Here we develop a mathematical model to establish the relationship between the number of type of words
(vocabulary) and the number of words sampled (text-length) for CDSs, when non-overlapping nucleotide strings with the same
length are treated as words. We use tangent-hyperbolic function, which captures the saturation property of vocabulary. Based
on the parameters of the model, we formulate a mathematical equation, known as “equation of word organization”, whose parameters essentially indicate that nucleotide organization of coding sequences are different from one another.
We also compare the word organization of CDSs with the random word distribution and conclude that a CDS is neither similar
to a natural human language nor to a random one. Moreover, these sequences have their unique nucleotide organization and it
is completely structured for specific biological functioning.
IM and AS contributed equally to this work. 相似文献
14.
G protein-coupled inwardly rectifying potassium channels, GIRK/Kir3.x, are gated by the Gbetagamma subunits of the G protein. The molecular mechanism of gating was investigated by employing a novel yeast-based random mutagenesis approach that selected for channel mutants that are active in the absence of Gbetagamma. Mutations in TM2 were found that mimicked the Gbetagamma-activated state. The activity of these channel mutants was independent of receptor stimulation and of the availability of heterologously expressed Gbetagamma subunits but depended on PtdIns(4,5)P(2). The results suggest that the TM2 region plays a key role in channel gating following Gbetagamma binding in a phospholipid-dependent manner. This mechanism of gating in inwardly rectifying K+ channels may be similar to the involvement of the homologous region in prokaryotic KcsA potassium channel and, thus, suggests evolutionary conservation of the gating structure. 相似文献
15.
Yu. V. Mamkaev 《Paleontological Journal》2010,44(12):1509-1517
The development of evolutionary theory requires the resolution of the problem of relationships between random and regular
processes in historical development of biological systems. According to the theory of natural selection, ecological factors
play a leading role in evolution. Variations are nondirectional, unpredictable, and provide chaotic diversity of variants,
only some of which are potentially useful. However, based on random processes, new variants that are useful for organisms
and remain adaptive significance in various ecological situations are infrequent. At the same time, morphology demonstrates
certain evolutionary patterns. The morphological approach takes into account the role in evolution of structural features
of organism and social systems and evolutionary significance of “constructive technologies,” which distinguish morphological
interpretation of evolutionary processes. The constructive and evolutionary patterns revealed in biological systems provide
the basis for morphological interpretation of the principle of natural selection: both natural and artificial selection is
interaction between social systems (populations, ecosystems, biogeocoenoses) and organisms composing them. 相似文献
16.
Tennessen JA 《Journal of molecular evolution》2005,61(4):445-455
Nonrandom patterns associated with adaptively evolving genes can shed light on how selection and mutation produce rapid changes
in sequences. I examine such patterns in two independent families of antimicrobial peptide genes: those in frogs, which are
known to have evolved under positive selection, and those in flatfishes, which I show have also evolved under positive selection.
I address two recently proposed hypotheses about the molecular evolution of antimicrobial peptide genes. The first is that
the mature peptide region is replicated by an error-prone polymerase that increases the mutation rate and the transversion/transition
ratio compared to the signal sequence of the same genes. The second is that mature peptides evolve in a coordinated fashion
with their propieces, such that a change in net charge in one molecular region prompts an opposite change in charge in the
other region. I test these hypotheses using alternative methods that minimize alignment errors, correct for phylogenetic nonindependence,
reduce sequence saturation, and account for differing selection pressures on different regions of the gene. In both gene families
I show that divergence at both synonymous and nonsynonymous sites within the mature peptide region is enhanced. However, in
neither gene family is there evidence of an increased mutational transversion/transition ratio or coordinated evolution. My
observations are consistent with either an elevated mutation rate in an adaptively evolving gene region or widespread selection
on “silent” sites. These hypotheses challenge the assumption that mutations are random and can be measured by the synonymous
substitution rate.
[Reviewing Editor: Dr. Willie J. Swanson] 相似文献
17.
The protein antibiotic colicin N forms ion-permeable channels through planar lipid bilayers. Channels are induced when positive
voltages higher than +60 mV are applied. Incorporated channels activate and inactivate in a voltage-dependent fashion. It
is shown that colicin N undergoes a transition between an “acidic” and a “basic” channel form which are distinguishable by
different voltage dependences. The single-channel conductance is non-ohmic and strongly dependent on pH, indicating that titratable
groups control the passage of ions through the channel. The ion selectivity of colicin N channels is influenced by the pH
and the lipid composition of the bilayer membrane. In neutral membranes the channel undergoes a transition from slightly cation-selective
to slightly anion-selective when the pH is changed from 7 to 5. In lipid membranes bearing a negative surface charge the channel
shows a more pronounced cation selectivity which decreases but does not reverse upon lowering the pH from 7 to 5. The high
degree of similarity between the channel characteristics of colicin A and N suggests that the channels share common features
in their molecular structure.
Offprint requests to: F. Pattus 相似文献
18.
This article is a review of scientific publications, in which issues of pathogenetics of multifactorial diseases (MFDs) are
considered from the viewpoint of evolution and ontogeny. Concepts explaining significance of evolutionary processes in the
formation of genetic architecture of human chronic diseases (“thrifty” genomes and phenotypes, “drifty genes,” decanalization)
are analyzed. The roles of natural selection and genetic drift in the formation of hereditary diversity of genes for susceptibility
to MFDs are considered. The modern concept of “disease ontogeny” (somatic mosaicism, loss of heterozygosity, paradominant
inheritance, epigenetic variability) is discussed. It is demonstrated that the evolutionary and ontogenetic approaches to
analysis of genimuc and other “-omic” data are essential for understanding the biology of diseases. 相似文献
19.
Extending Darwin’s analogy: Bridging differences in concepts of selection between farmers, biologists, and plant breeders 总被引:1,自引:0,他引:1
Darwin developed his theory of evolution based on an analogy between artificial selection by breeders of his day and “natural
selection.” For Darwin, selection included what biologists came to see as being composed of (1) phenotypic selection of individuals
based on phenotypic differences, and, when these are based on heritable genotypic differences, (2) genetic response between
generations, which can result in (3) evolution (cumulative directional genetic response over generations). The use of the
term “selection” in biology and plant breeding today reflects Darwin’s assumption—phenotypic selection is only biologically
significant when it results in evolution. In contrast, research shows that small-scale, traditionally-based farmers select
seed as part of an integrated production and consumption system in which selection is often not part of an evolutionary process,
but is still useful to farmers. Extending Darwin’s analogy to farmers can facilitate communication between farmers, biologists,
and plant breeders to improve selection and crop genetic resource conservation. 相似文献
20.
Rodrigo Scheihing Pedro Labarca Leyla Cardenas Roberto F. Nespolo 《Hydrobiologia》2011,671(1):193-203
One of the most important research topics in evolutionary ecology is body size evolution. Actually, several hypotheses have
been proposed to explain the many observed patterns—also known as “rules”—of body size variation in across latitude, temperature,
and time. The temperature–size rule (TSR), describes an inverse relationship between body size and temperature. We took advantage
of the “natural laboratory” that the crustacean populations at the Chilean altiplano offers, to study the TSR in ostracods.
We studied three populations of Limnocythere atacamae that are physically separated by several kilometers, and differ mainly by their permanent thermal regime. We found larger
individuals in the hotspring compared to the cold ponds. Also, in the hotspring we found a significant quadratic selection
coefficient, suggesting stabilizing selection in this population. The fitness profiles showed stabilizing selection in the
hotspring, and positive directional selection in the ponds. Our results suggest the existence of an optimal body size above
the population means. This optimal size is apparently attained in the hotspring population. Then, natural selection appears
to be promoting a shift in the mean phenotype that, for some reason, is not attained in the cold environments. Genetic slippage
and population bottleneck would explain this absence of response to selection. 相似文献