共查询到20条相似文献,搜索用时 78 毫秒
1.
Robert G. Beiko 《Biology & philosophy》2010,25(4):659-673
Frequent lateral genetic transfer undermines the existence of a unique “tree of life” that relates all organisms. Vertical
inheritance is nonetheless of vital interest in the study of microbial evolution, and knowing the “tree of cells” can yield
insights into ecological continuity, the rates of change of different cellular characters, and the evolutionary plasticity
of genomes. Notwithstanding within-species recombination, the relationships most frequently recovered from genomic data at
shallow to moderate taxonomic depths are likely to reflect cellular inheritance. At the same time, it is clear that several
types of ‘average signals’ from whole genomes can be highly misleading, and the existence of a central tendency must not be
taken as prima facie evidence of vertical descent. Phylogenetic networks offer an attractive solution, since they can be formulated in ways that
mitigate the misleading aspects of hybrid evolutionary signals in genomes. But the connections in a network typically show
genetic relatedness without distinguishing between vertical and lateral inheritance of genetic material. The solution may
lie in a compromise between strict tree-thinking and network paradigms: build a phylogenetic network, but identify the set
of connections in the network that are potentially due to vertical descent. Even if a single tree cannot be unambiguously
identified, choosing a subnetwork of putative vertical connections can still lead to drastic reductions in the set of candidate
vertical hypotheses. 相似文献
2.
While self-assembly is a fairly active area of research in swarm intelligence, relatively little attention has been paid to
the issues surrounding the construction of network structures. In this paper we extend methods developed previously for controlling
collective movements of agent teams to serve as the basis for self-assembly or “growth” of networks, using neural networks
as a concrete application to evaluate our approach. Our central innovation is having network connections arise as persistent
“trails” left behind moving agents, trails that are reminiscent of pheromone deposits made by agents in ant colony optimization
models. The resulting network connections are thus essentially a record of agent movements. We demonstrate our model’s effectiveness
by using it to produce two large networks that support subsequent learning of topographic and feature maps. Improvements produced
by the incorporation of collective movements are also examined through computational experiments. These results indicate that
methods for directing collective movements can be adopted to facilitate network self-assembly. 相似文献
3.
We study how individual memory items are stored assuming that situations given in the environment can be represented in the
form of synaptic-like couplings in recurrent neural networks. Previous numerical investigations have shown that specific architectures
based on suppression or max units can successfully learn static or dynamic stimuli (situations). Here we provide a theoretical
basis concerning the learning process convergence and the network response to a novel stimulus. We show that, besides learning
“simple” static situations, a nD network can learn and replicate a sequence of up to n different vectors or frames. We find limits on the learning rate and show coupling matrices developing during training in
different cases including expansion of the network into the case of nonlinear interunit coupling. Furthermore, we show that
a specific coupling matrix provides low-pass-filter properties to the units, thus connecting networks constructed by static
summation units with continuous-time networks. We also show under which conditions such networks can be used to perform arithmetic
calculations by means of pattern completion. 相似文献
4.
Kano H Kurosawa K Horii E Ikegawa S Yoshikawa H Kurahashi H Toda T 《Human genetics》2005,118(3-4):477-483
Split-hand/split-foot malformation (SHFM) is a congenital limb malformation characterized by a median cleft of hand and/or foot due to the absence of central rays. Five loci for syndromic and non-syndromic SHFM, termed SHFM1-5, have been mapped to date. Recently, a 0.5 Mb tandem genomic duplication was found at chromosome 10q24 in SHFM3 families. To refine the minimum duplicated region and to further characterize the SHFM3 locus, we screened 28 non-syndromic SHFM families for tandem genomic duplication of 10q24 by Southern blot and sequence analysis of the dactylin gene. Of 28 families, only two showed genomic rearrangements. Representative patients from the two families exhibit typical SHFM, with symmetrically affected hands and feet. One patient is a familial case with a 511,661 bp tandem duplication, whereas the second is a sporadic case arising from a de novo, 447,338 bp duplication of maternal origin. The smaller duplication in the second patient contained the LBX1, BTRC, POLL, and DPCD genes and a disrupted extra copy of the dactylin gene, and was nearly identical to the smallest known duplicated region of SHFM3. Our results indicate that genomic rearrangement of SHFM3 is rare among non-syndromic SHFM patients and emphasize the importance of screening for genomic rearrangements even in sporadic cases of SHFM. 相似文献
5.
Daniel J. Sargent Annalisa Marchese David W. Simpson Werner Howad Felicidad Fernández-Fernández Amparo Monfort Pere Arús Kate M. Evans Kenneth R. Tobutt 《Tree Genetics & Genomes》2009,5(1):133-145
The Rosaceae contains many economically valuable crop genera, including Malus (apple), Fragaria (strawberry), and Prunus (stone fruit). There has been increasing interest in the development of linkage maps for these species, with a view to marker-assisted
selection to assist breeding programs and, recently, in the development of transferable markers to permit syntenic comparisons
of maps of different rosaceous genera. In this investigation, a set of Malus cDNA sequences were downloaded from the European Molecular Biology Laboratory database. The sequences were aligned with homologous
full-length Arabidopsis genomic DNA sequences to identify putative intron–exon junctions and conserved flanking exon sequences. Primer pairs were
designed from the conserved exon sequences flanking predicted intron–exon junctions in the Malus cDNA sequences. These were used to amplify products by polymerase chain reaction from the parents of the Malus mapping progeny “Fiesta” × “Totem.” Eleven loci, representing ten genes (39%), were polymorphic in the “Fiesta” × “Totem”
population and mapped to seven Malus linkage groups. Transferability to other rosaceous genera was high, with primer pairs representing 85% of genes, amplifying
products from Fragaria and primer pairs representing 85% of genes, amplifying products from Prunus genomic DNA. These primers were screened in the Fragaria and Prunus mapping bin sets and 38% of the genes were successfully located on both maps. Analysis of the markers mapped in more than
one rosaceous genus revealed patterns of synteny between genera, while a comparison with the physical positions of homologous
genes on the Arabidopsis genome revealed high sequence conservation but only fragmentary patterns of macrosynteny. 相似文献
6.
Urm1 (ubiquitin-related modifier), involved in diverse biological processes in yeast, is proved to be a “molecular fossil”
in ubiquitin superfamily. Here we report the resonance assignment of Urm1 from Trypanosoma brucei. 相似文献
7.
Dynamical behavior of a biological neuronal network depends significantly on the spatial pattern of synaptic connections among
neurons. While neuronal network dynamics has extensively been studied with simple wiring patterns, such as all-to-all or random
synaptic connections, not much is known about the activity of networks with more complicated wiring topologies. Here, we examined
how different wiring topologies may influence the response properties of neuronal networks, paying attention to irregular
spike firing, which is known as a characteristic of in vivo cortical neurons, and spike synchronicity. We constructed a recurrent network model of realistic neurons and systematically
rewired the recurrent synapses to change the network topology, from a localized regular and a “small-world” network topology
to a distributed random network topology. Regular and small-world wiring patterns greatly increased the irregularity or the
coefficient of variation (Cv) of output spike trains, whereas such an increase was small in random connectivity patterns.
For given strength of recurrent synapses, the firing irregularity exhibited monotonous decreases from the regular to the random
network topology. By contrast, the spike coherence between an arbitrary neuron pair exhibited a non-monotonous dependence
on the topological wiring pattern. More precisely, the wiring pattern to maximize the spike coherence varied with the strength
of recurrent synapses. In a certain range of the synaptic strength, the spike coherence was maximal in the small-world network
topology, and the long-range connections introduced in this wiring changed the dependence of spike synchrony on the synaptic
strength moderately. However, the effects of this network topology were not really special in other properties of network
activity.
Action Editor: Xiao-Jing Wang 相似文献
8.
Parent-specific, randomly amplified polymorphic DNA (RAPD) markers were obtained from total genomic DNA ofChlamydomonas reinhardtii. Such parent-specific RAPD bands (genomic fingerprints) segregated uniparentally (through mt+) in a cross between a pair of polymorphic interfertile strains ofChlamydomonas (C. reinhardtii andC. minnesotti), suggesting that they originated from the chloroplast genome. Southern analysis mapped the RAPD-markers to the chloroplast
genome. One of the RAPD-markers, “P2” (1.6 kb) was cloned, sequenced and was fine mapped to the 3 kb region encompassing 3′
end of 23S, full 5S and intergenic region between 5S and psbA. This region seems divergent enough between the two parents,
such that a specific PCR designed for a parental specific chloroplast sequence within this region, amplified a marker in that
parent only and not in the other, indicating the utility of RAPD-scan for locating the genomic regions of sequence divergence.
Remarkably, the RAPD-product, “P2” seems to have originated from a PCR-amplification of a much smaller (about 600 bp), but
highly repeat-rich (direct and inverted) domain of the 3 kb region in a manner that yielded no linear sequence alignment with
its own template sequence. The amplification yielded the same uniquely “sequence-scrambled” product, whether the template
used for PCR was total cellular DNA, chloroplast DNA or a plasmid clone DNA corresponding to that region. The PCR product,
a "unique" new sequence, had lost the repetitive organization of the template genome where it had originated from and perhaps
represented a “complex path” of copy-choice replication. 相似文献
9.
N. Rashevsky 《Bulletin of mathematical biology》1967,29(3):643-648
In continuation of previous studies (Bull. Math. Biophysics,28, 283–308; 655–661, 1966;29, 139–152, 1967) it is shown that the difference between the “metric” aspects of physics and the “relational” aspects of biological
and social sciences disappear by accepting the broader definition of “relation”, such as that given in mathematics and logic.
A conceptual superstructure then becomes possible from which all three branches of knowledge may be derived, though none of
them can be derived from the others. 相似文献
10.
11.
Gopalkrishnan M 《Bulletin of mathematical biology》2011,73(12):2962-2982
We define catalytic networks as chemical reaction networks with an essentially catalytic reaction pathway: one which is “on” in the presence of certain
catalysts and “off” in their absence. We show that examples of catalytic networks include synthetic DNA molecular circuits
that have been shown to perform signal amplification and molecular logic. Recall that a critical siphon is a subset of the species in a chemical reaction network whose absence is forward invariant and stoichiometrically compatible
with a positive point. Our main theorem is that all weakly-reversible networks with critical siphons are catalytic. Consequently,
we obtain new proofs for the persistence of atomic event-systems of Adleman et al., and normal networks of Gnacadja. We define
autocatalytic networks, and conjecture that a weakly-reversible reaction network has critical siphons if and only if it is autocatalytic. 相似文献
12.
We recently classified 23 bacteria into two types based on their complete genomes; “S-type” as represented by Staphylococcus aureus and “E-type” as represented by Escherichia coli. Classification was characterized by concentrations of Arg, Ala or Lys in the amino acid composition calculated from the
complete genome. Based on these previous classifications, not only prokaryotic but also eukaryotic genome structures were
investigated by amino acid compositions and nucleotide contents. Organisms consisting of 112 bacteria, 15 archaea and 18 eukaryotes
were classified into two major groups by cluster analysis using GC contents at the three codon positions calculated from complete
genomes. The 145 organisms were classified into “AT-type” and “GC-type” represented by high A or T (low G or C) and high G
or C (low A or T) contents, respectively, at every third codon position. Reciprocal changes between G or C and A or T contents
at the third codon position occurred almost synchronously in every codon among the organisms. Correlations between amino acid
concentrations (Ala, Ile and Lys) and the nucleotide contents at the codon position were obtained in both “AT-type” and “GC-type”
organisms, but with different regression coefficients. In certain correlations of amino acid concentrations with GC contents,
eukaryotes, archaea and bacteria showed different behaviors; thus these kingdoms evolved differently. All organisms are basically
classifiable into two groups having characteristic codon patterns; organisms with low GC and high AT contents at the third
codon position and their derivatives, and organisms with an inverse relationship. 相似文献
13.
N. Rashevsky 《Bulletin of mathematical biology》1966,28(4):655-661
The paper develops further some suggestions made previously (Bulletin of Mathematical Biophysics,28, 283–308, 1966) that certain biological phenomena may be more easily interpreted from a “sociological” point of view by considering
the organism as a social aggregate of cells and a cell as a social aggregate of genes. In this light the problems of origin
of life on earth, of aging, and of parasitism and symbiosis are discussed. The notion of social aggregates of different orders
is introduced. 相似文献
14.
M. H. Tixier P. Sourdille G. Charmet G. Gay C. Jaby T. Cadalen S. Bernard P. Nicolas M. Bernard 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1998,97(7):1076-1082
An intervarietal molecular-marker map was used for the detection of genomic regions influencing crossability between wheat
(Triticum aestivum L. em Thell) and rye (Secale cereale L.). Analysis of deviance and logistic marker-regression methods were conducted on data from doubled haploid lines from a
cross between “Courtot” and “Chinese Spring”. A major quantitative trait locus (QTL) involved in crossability, associated
with the marker Xfba367-5B, was detected on the short arm of chromosome 5B. An additional locus, Xwg583-5B, was indicated on the long arm of chromosome 5B. This minor QTL might correspond to Kr1 which was presumed to be the major gene controlling crossability. Another locus of the genome, Xtam51-7A on chromosome 7A, was significantly associated with this trait. Alleles of “non-crossability” were contributed by the non-crossable
cultivar “Courtot”. The three-marker model explains 65% of the difference in crossability between the two parents. The present
results are discussed in relation to those previously carried out to locate the Kr genes by using the telocentric mapping technique.
Received: 27 February 1998 / Accepted: 15 May 1998 相似文献
15.
16.
Dadkhodaie NA Karaoglou H Wellings CR Park RF 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2011,122(3):479-487
The rust resistance genes Lr53 and Yr35, transferred to common wheat from Triticum dicoccoides, were reported previously to be completely linked on chromosome 6B. Four F
3 families were produced from a cross between a line carrying Lr53 and Yr35 (98M71) and the leaf rust and stripe rust susceptible genotype Avocet “S” and were rust tested using Puccinina triticina pathotype 53-1,(6),(7),10,11 and Puccinia striiformis f. sp. tritici pathotype 110 E143 A+. The homozygous resistant lines produced infection types of “;1−” and “;N” to these pathotypes, respectively.
The Chi-squared tests indicated goodness-of-fit of the data for one leaf rust gene and one stripe rust gene segregation. Linkage
analysis using this population demonstrated recombination of 3% between the genes. Microsatellite markers located on the short
arm of chromosome 6B were used to map the genes, with the markers cfd1 and gwm508 being mapped approximately 1.1 and 4.5 cM, respectively, proximal to Lr53. Additional studies of the relationship between Lr36, also located on the short arm of chromosome 6B, and Lr53 indicated that the two genes were independent. 相似文献
17.
Protein interaction networks in plants 总被引:3,自引:0,他引:3
Protein–protein interactions are fundamental to virtually every aspect of cellular functions. With the development of high-throughput technologies of both the yeast two-hybrid system and tandem mass spectrometry, genome-wide protein-linkage mapping has become a major objective in post-genomic research. While at least partial “interactome” networks of several model organisms are already available, in the plant field, progress in this respect is slow. However, even with comprehensive protein interaction data still missing, substantial recent advance in the graph-theoretical functional interpretation of complex network architectures might pave the way for novel approaches in plant research. This article reviews current progress and discussions in network biology. Emphasis is put on the question of what can be learned about protein functions and cellular processes by studying the topology of complex protein interaction networks and the evolutionary mechanisms underlying their development. Particularly the intermediate and local levels of network organization—the modules, motifs and cliques—are increasingly recognized as the operational units of biological functions. As demonstrated by some recent results from systematic analyses of plant protein families, protein interaction networks promise to be a valuable tool for a molecular understanding of functional specificities and for identifying novel regulatory components and pathways. 相似文献
18.
Rimoldi S Papis E Bernardini G Prati M Gornati R 《Molecular and cellular biochemistry》2007,301(1-2):143-153
GD3, a minor ganglioside in most normal tissues, is involved in important biological events and its expression could increase
in pathological conditions. Organism integrity requires a tight balance between the anabolic and catabolic processes, thus
it is important to control the intracellular expression of those “key” enzymes, which act at the “branching point” of ganglioside
metabolism; one of these is the GD3-synthase (ST8Sia I). In this paper, we report the sequences of two ST8Sia I mRNAs found
in Xenopus laevis and their genomic organization; the canonical form resulted constituted of 5 exons and 4 introns, while the “short” mRNA
lacks of the exon 2. The expression of the two ST8Sia I mRNAs during embryo development and their tissue distribution in adult
animals showed the single or simultaneous presence of the two forms. Experiments of in vitro expression and evaluation of
enzymatic activity of the two hypothetical proteins turned out to be ST8Sia I. In the end, considering the growing interest
toward the specie Xenopus tropicalis, due to its diploid genome that render it more suitable for genetic studies, we also cloned X. tropicalis ST8Sia I.
Accession numbers: AY272057, AY272056 相似文献
19.
Leptospirillum ferriphilum has been identified as the dominant, moderately thermophilic, bioleaching microorganism in bioleaching processes. It is an
acidic and chemolithoautrophic bacterium that gains electrons from ferrous iron oxidation for energy production and cell growth.
Genetic information about this microorganism has been limited until now, which has hindered its further exploration. In this
study, the complete genome of L. ferripilum ML-04 is sequenced and annotated. The bacterium has a single circular chromosome of 2,406,157 bp containing 2,471 coding
sequences (CDS), 2 rRNA operons, 48 tRNA genes, a large number of mobile genetic elements and 2 genomic islands. In silico analysis shows L. ferriphilum ML-04 fixes carbon through a reductive citric acid (rTCA) cycle, and obtains nitrogen through ammonium assimilation. The
genes related to “cell envelope biogenesis, outer membrane” (6.9%) and “DNA replication, recombination and repair” (5.6%)
are abundant, and a large number of genes related to heavy metal detoxification, oxidative and acidic stress defense, and
signal transduction pathways were detected. The genomic plasticity, plentiful cell envelope components, inorganic element
metabolic abilities and stress response mechanisms found the base for this organism’s survival in the bioleaching niche. 相似文献
20.
Masazumi Mitani 《Primates; journal of primatology》1986,27(4):397-412
Japanese monkeys often exchange the particular vocal sound, “coo,” especially when they feed or move as a group. It was considered
that the “coo” sound had no positive social meaning, perhaps because the “coo” sound network and its function were hidden
behind other behavioral observations. For identification of the vocalizer only from hearing the “coo” sound, three phonetic
values, i.e., the “fundamental,” “duration,” and “formants,” plus other characteristics were used as indices of voiceprints. The results indicated that these were effective for identifying
the vocalizer in two-thirds of the adults in the study troop which was composed of 12 adults and 16 immature members. The
“coo” sound exchange network among the troop members (adults) was drawn on the basis of the voiceprint identification. The
network showed three characteristics as follows: (1) matriarchs of the kin-groups frequently exchanged “coo” sounds with each
other; (2) the other females exchanged “coo” sounds mostly within their own kin-groups; and (3) males seldom participated
in the “coo” sound exchange. This suggests that “coo” sound exchange plays a central role for the matriarch of kin-groups
in binding each kin-group and, ultimately, in binding all members together into an organized troop. 相似文献