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Comparative analysis indicates regulatory neofunctionalization of yeast duplicates
Itay Tirosh, Naama Barkai
Genome Biology , 2007, DOI: 10.1186/gb-2007-8-4-r50
Abstract: We developed a novel method to compare expression profiles from different organisms and applied it to analyze the expression divergence of yeast duplicated genes. The expression profiles of Saccharomyces cerevisiae duplicate pairs were compared with those of their pre-duplication orthologs in Candida albicans. Duplicate pairs were classified into two classes, corresponding to symmetric versus asymmetric rates of expression divergence. The latter class includes 43 duplicate pairs in which only one copy has a significant expression similarity to the C. albicans ortholog. These may present cases of regulatory neofunctionalization, as supported also by their dispensability and variability.Duplicated genes may diversify through regulatory neofunctionalization. Notably, the asymmetry of gene sequence evolution and the asymmetry of gene expression evolution are only weakly correlated, underscoring the importance of expression analysis to elucidate the evolution of novel functions.Current genomes were shaped by numerous duplications of single genes, chromosomal segments and even entire genomes [1-3]. In most cases, one copy of the duplicated gene is rapidly lost either by deletion or through mutations ('nonfunctionalization'), reflecting the lack of selection for each individual copy. In other cases, however, both duplicates may survive despite the initial redundancy and become fixed in the genome. The retention of both duplicates over millions of years implies that they confer an advantage such that deletion of either copy will cause a reduction in fitness.While the evolutionary advantage of duplicates retention is usually difficult to ascertain, several models have been suggested [4]. First, duplicates could be retained due to selection for robustness through redundancy [5], although this view has been frequently challenged [6,7]. Second, selection for high protein dosage may favor the presence of two gene copies [8]. In these cases, similarity between the two copies can
Recombination facilitates neofunctionalization of duplicate genes via originalization
Cheng Xue, Ren Huang, Shu-Qun Liu, Yun-Xin Fu
BMC Genetics , 2010, DOI: 10.1186/1471-2156-11-46
Abstract: Results show that through originalization recombination might not only shorten mean time to neofunctionalizaiton, but also enlarge Pneo.Therefore, recombination might facilitate neofunctionalization via originalization. Several extensive applications of these results on genomic evolution have been discussed: 1. Time to nonfunctionalization can be much longer than a few million generations expected before; 2. Homogenization on duplicated loci results from not only gene conversion, but also originalization; 3. Although the rate of advantageous mutation is much small compared with that of degenerative mutation, Pneo cannot be expected to be small.Gene duplication is the most common way of evolving new genes [1-4], but it is still argued how new genes evolve from duplicate genes in detail [5-7]. Ohno (1970) proposed that new genes might be fixed at one of duplicated loci by genetic drift, which was called neofunctionalization. Because degenerative mutations might also be fixed on the duplicated loci (called nonfunctionalization) and the occurring rate of degenerative mutation is usually much larger than that of advantageous mutation, the evolutionary fate of most duplicate genes is nonfunctionalization [8]. However, it has been observed that many duplicate genes are retained in some genomes, such as in tetraploid fish [9], Xenopus Laevis [10], and yeast Saccharomyces cerevisiae [4,11,12]. So it is necessary to explain these observations reasonably.Assuming double null recessive selection and unlinked duplicated loci, Walsh (1995 and 2003) modeled the state of the population as a three-state (wild-type, degenerative and advantageous alleles) Markov chain, and thus calculated the probability (Pneo) that the advantageous allele will fix before the nonfunctional allele does [13,14]. Under weak positive selection (roughly Ns < < 1), Pneo was given bywhere EXP is the exponential function, ρ is the ratio of advantageous mutation rate (μneo) to degenerative mutation rate (μnon)
Subfunctionalization of duplicated genes as a transition state to neofunctionalization
Shruti Rastogi, David A Liberles
BMC Evolutionary Biology , 2005, DOI: 10.1186/1471-2148-5-28
Abstract: A set of lattice model genes that fold and bind to two peptide ligands with overlapping binding pockets, but not a third ligand present in the cell was designed. Each gene was duplicated in a model haploid species with a small constant population size and no recombination. One set of models allowed subfunctionalization of binding events following duplication, while another set did not allow subfunctionalization. Modeling under such conditions suggests that subfunctionalization plays an important role, but as a transition state to neofunctionalization rather than as a terminal fate of duplicated genes. There is no apparent selective pressure to maintain redundancy.Subfunctionalization results in an increase in the preservation of duplicated gene copies, including those that are neofunctionalized, but never represents a substantial fraction of duplicate gene copies at any evolutionary time point and ultimately leads to neofunctionalization of those preserved copies. This conclusion also may reflect changes in gene function after duplication with time in real genomes.A number of mechanisms can generate duplicate copies of genes, ranging from single gene duplications to regional and whole genome duplications [1-3]. Large increases in gene number have been coupled to increases in organismal complexity and radiative divergence at several points in the history of metazoans including during the chordate/vertebrate transition and during the teleost fish divergence [1,4,5].Metazoans differ from prokaryotes in their much smaller effective population sizes, where theory predicts that neutral stochastic processes will be relatively more important than adaptive processes in the expected case that adaptive mutations are rarer than nearly neutral mutations [6]. Large scale analyses, based upon the ratio of nonsynonymous to synonymous nucleotide substitution rates [7] or MacDonald-Kreitman statistics [8] have indicated small to intermediate degrees of positive selection (adaptive su
Neofunctionalization in Vertebrates: The Example of Retinoic Acid Receptors  [PDF]
Hector Escriva,Stéphanie Bertrand equal contributor,Pierre Germain equal contributor,Marc Robinson-Rechavi,Muriel Umbhauer,Jér?me Cartry,Marilyne Duffraisse,Linda Holland,Hinrich Gronemeyer,Vincent Laudet
PLOS Genetics , 2006, DOI: 10.1371/journal.pgen.0020102
Abstract: Understanding the role of gene duplications in establishing vertebrate innovations is one of the main challenges of Evo-Devo (evolution of development) studies. Data on evolutionary changes in gene expression (i.e., evolution of transcription factor-cis-regulatory elements relationships) tell only part of the story; protein function, best studied by biochemical and functional assays, can also change. In this study, we have investigated how gene duplication has affected both the expression and the ligand-binding specificity of retinoic acid receptors (RARs), which play a major role in chordate embryonic development. Mammals have three paralogous RAR genes—RARα, β, and γ—which resulted from genome duplications at the origin of vertebrates. By using pharmacological ligands selective for specific paralogues, we have studied the ligand-binding capacities of RARs from diverse chordates species. We have found that RARβ-like binding selectivity is a synapomorphy of all chordate RARs, including a reconstructed synthetic RAR representing the receptor present in the ancestor of chordates. Moreover, comparison of expression patterns of the cephalochordate amphioxus and the vertebrates suggests that, of all the RARs, RARβ expression has remained most similar to that of the ancestral RAR. On the basis of these results together, we suggest that while RARβ kept the ancestral RAR role, RARα and RARγ diverged both in ligand-binding capacity and in expression patterns. We thus suggest that neofunctionalization occurred at both the expression and the functional levels to shape RAR roles during development in vertebrates.
Ubiquity and a general logarithm law for geodesics  [PDF]
Victor Beresnevich,Sanju Velani
Mathematics , 2007,
Abstract: There are two fundamental results in the classical theory of metric Diophantine approximation: Khintchine's theorem and Jarnik's theorem. The former relates the size of the set of well approximable numbers, expressed in terms of Lebesgue measure, to the behavior of a certain volume sum. The latter is a Hausdorff measure version of the former. We start by discussing these theorems and show that they are both in fact a simple consequence of the notion of `local ubiquity'. The local ubiquity framework introduced here is a much simplified and more transparent version of that in \cite{memoirs}. Furthermore, it leads to a single local ubiquity theorem that unifies the Lebesgue and Hausdorff theories. As an application of our framework we consider the theory of metric Diophantine approximation on limit sets of Kleinian groups. In particular, we obtain a general Hausdorff measure version of Sullivan's logarithm law for geodesics -- an aspect overlooked in \cite{memoirs}.
The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?
Véronique Douard, Frédéric Brunet, Bastien Boussau, Isabelle Ahrens-Fath, Virginie Vlaeminck-Guillem, Bernard Haendler, Vincent Laudet, Yann Guiguen
BMC Evolutionary Biology , 2008, DOI: 10.1186/1471-2148-8-336
Abstract: In this paper, we studied in a wide range of Actinopterygians the duplication and fate of the androgen receptor (AR, NR3C4), a nuclear receptor known to play a key role in sex-determination in vertebrates. The pattern of AR gene duplication is consistent with an early WGD event: it has been duplicated into two genes AR-A and AR-B after the split of the Acipenseriformes from the lineage leading to teleost fish but before the divergence of Osteoglossiformes. Genomic and syntenic analyses in addition to lack of PCR amplification show that one of the duplicated copies, AR-B, was lost in several basal Clupeocephala such as Cypriniformes (including the model species zebrafish), Siluriformes, Characiformes and Salmoniformes. Interestingly, we also found that, in basal teleost fish (Osteoglossiformes and Anguilliformes), the two copies remain very similar, whereas, specifically in Percomorphs, one of the copies, AR-B, has accumulated substitutions in both the ligand binding domain (LBD) and the DNA binding domain (DBD).The comparison of the mutations present in these divergent AR-B with those known in human to be implicated in complete, partial or mild androgen insensitivity syndrome suggests that the existence of two distinct AR duplicates may be correlated to specific functional differences that may be connected to the well-known plasticity of sex determination in fish. This suggests that three specific events have shaped the present diversity of ARs in Actinopterygians: (i) early WGD, (ii) parallel loss of one duplicate in several lineages and (iii) putative neofunctionalization of the same duplicate in percomorphs, which occurred a long time after the WGD.Actinopterygian fishes have provided the first clear demonstration of an ancient whole genome duplication (WGD) in vertebrate evolution [1]. This event was originally suggested based on the finding that zebrafish and medaka possess seven Hox clusters [2-4], compared to four in mammals and one in most invertebrates. It
An Analysis of College English Classroom Questioning  [cached]
Weihua Yu
Journal of Language Teaching and Research , 2010, DOI: 10.4304/jltr.1.2.136-144
Abstract: The analysis of classroom interaction is a very important form which classroom process research has taken. The present study focuses on college English classroom questioning. Through a detailed description and analysis of the collected data, types of questions and modification techniques are made clear and on the basis of which a few strategies for college English teachers are put forward by the author in order to improve college English teaching and learning.
Analysis of questioning technique during classes in medical education
Young Hye Cho, Sang Yeoup Lee, Dong Wook Jeong, Sun Ju Im, Eun Jung Choi, Sun Hee Lee, Sun Yong Baek, Yun Jin Kim, Jeong Gyu Lee, Yu Hyone Yi, Mi Jin Bae, So Jung Yune
BMC Medical Education , 2012, DOI: 10.1186/1472-6920-12-39
Abstract: Data on the perceptions of the questioning skills used during lectures was collected using a self?questionnaire for faculty members (N?=?33) during the second semester of 2008. The questionnaire consisted of 18 items covering the awareness and characteristics of questioning skills. Recorded video tapes were used to observe the faculty members’ questioning skills.Most faculty members regarded the questioning technique during classes as being important and expected positive outcomes in terms of the students’ participation in class, concentration in class and understanding of the class contents. In the 99 classes analyzed, the median number of questions per class was 1 (0–29). Among them, 40 classes (40.4?%) did not use questioning techniques. The frequency of questioning per lecture was similar regardless of the faculty members’ perception. On the other hand, the faculty members perceived that their usual wait time after question was approximately 10 seconds compared to only 2.5 seconds measured from video analysis. More lecture?experienced faculty members tended to ask more questions in class.There were some discrepancies regarding the questioning technique between the faculty members’ perceptions and reality, even though they had positive opinions of the technique. The questioning skills during a lecture need to be emphasized to faculty members.
Questioning-Based Learning in History Education
Rüstü YE??L
Journal of Kirsehir Education Faculty , 2010,
Abstract: Learning approach based on questioning which could be applied in history teaching is stressed in this study. History learning based on questioning is an approach which includes the efforts of learning history by questioning and asking questions as a historian. The studies on education sciences and history education are searched; and principles which could guide history teachers to make use of the students’ questions and questioning in history and bringing in the students, are tried to be determined. At the end of this study,to make the students acquire these skills, eight principles were determined to guide the history teachers. To be able to make this approach applied in history education, history teachers should structure history education applications in accordance with modern and scientific developments by reflecting the determined principles on the applications.
Describability via ubiquity and eutaxy in Diophantine approximation  [PDF]
Arnaud Durand
Mathematics , 2015,
Abstract: We present a comprehensive framework for the study of the size and large intersection properties of sets of limsup type that arise naturally in Diophantine approximation and multifractal analysis. This setting encompasses the classical ubiquity techniques, as well as the mass and the large intersection transference principles, thereby leading to a thorough description of the properties in terms of Hausdorff measures and large intersection classes associated with general gauge functions. The sets issued from eutaxic sequences of points and optimal regular systems may naturally be described within this framework. The discussed applications include the classical homogeneous and inhomogeneous approximation, the approximation by algebraic numbers, the approximation by fractional parts, the study of uniform and Poisson random coverings, and the multifractal analysis of L{\'e}vy processes.
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