Faculty Opinions recommendation of Gains and Losses of Cis-regulatory Elements Led to Divergence of the Arabidopsis APETALA1 and CAULIFLOWER Duplicate Genes in the Time, Space, and Level of Expression and Regulation of One Paralog by the Other.

Author(s):  
François Parcy
Genetics ◽  
1999 ◽  
Vol 151 (4) ◽  
pp. 1531-1545 ◽  
Author(s):  
Allan Force ◽  
Michael Lynch ◽  
F Bryan Pickett ◽  
Angel Amores ◽  
Yi-lin Yan ◽  
...  

Abstract The origin of organismal complexity is generally thought to be tightly coupled to the evolution of new gene functions arising subsequent to gene duplication. Under the classical model for the evolution of duplicate genes, one member of the duplicated pair usually degenerates within a few million years by accumulating deleterious mutations, while the other duplicate retains the original function. This model further predicts that on rare occasions, one duplicate may acquire a new adaptive function, resulting in the preservation of both members of the pair, one with the new function and the other retaining the old. However, empirical data suggest that a much greater proportion of gene duplicates is preserved than predicted by the classical model. Here we present a new conceptual framework for understanding the evolution of duplicate genes that may help explain this conundrum. Focusing on the regulatory complexity of eukaryotic genes, we show how complementary degenerative mutations in different regulatory elements of duplicated genes can facilitate the preservation of both duplicates, thereby increasing long-term opportunities for the evolution of new gene functions. The duplication-degeneration-complementation (DDC) model predicts that (1) degenerative mutations in regulatory elements can increase rather than reduce the probability of duplicate gene preservation and (2) the usual mechanism of duplicate gene preservation is the partitioning of ancestral functions rather than the evolution of new functions. We present several examples (including analysis of a new engrailed gene in zebrafish) that appear to be consistent with the DDC model, and we suggest several analytical and experimental approaches for determining whether the complementary loss of gene subfunctions or the acquisition of novel functions are likely to be the primary mechanisms for the preservation of gene duplicates. For a newly duplicated paralog, survival depends on the outcome of the race between entropic decay and chance acquisition of an advantageous regulatory mutation. Sidow (1996, p. 717) On one hand, it may fix an advantageous allele giving it a slightly different, and selectable, function from its original copy. This initial fixation provides substantial protection against future fixation of null mutations, allowing additional mutations to accumulate that refine functional differentiation. Alternatively, a duplicate locus can instead first fix a null allele, becoming a pseudogene. Walsh (1995, p. 426) Duplicated genes persist only if mutations create new and essential protein functions, an event that is predicted to occur rarely. Nadeau and Sankoff (1997, p. 1259) Thus overall, with complex metazoans, the major mechanism for retention of ancient gene duplicates would appear to have been the acquisition of novel expression sites for developmental genes, with its accompanying opportunity for new gene roles underlying the progressive extension of development itself. Cooke et al. (1997, p. 362)


Author(s):  
Stephen A. White

Any attempt to trace the origin of Greek philosophy faces two complementary problems. One is the fact that evidence for the early philosophers is woefully meager. The other problem raises a question of what is to be counted as philosophy. Yet neither problem is insuperable. This article proposes to reorient the search for origins in two ways, corresponding to these two problems. First, rather than trying to reconstruct vanished work directly, this article focuses on a crucial stage in its ancient reception, in particular, the efforts by Aristotle and his colleagues in the latter half of the fourth century to collect, analyze, and assess the evidence then available for earlier attempts to understand the natural world. The other shift in focus this article makes is from philosophy to science; or rather, it focuses on evidence for the interplay between observation, measurement, and explanation in the work of three sixth-century Milesians.


2014 ◽  
Vol 556-562 ◽  
pp. 1510-1514
Author(s):  
Li Qiang Lin ◽  
Hong Wen Yan

For the low efficiency in generating candidate item sets of apriori algorithm, this paper presents a method based on property division to improve generating candidate item sets. Comparing the improved apriori algorithm with the other algorithm and the improved algorithm is applied to the power system accident cases in extreme climate. The experiment results show that the improved algorithm significantly improves the time efficiency of generating candidate item sets. And it can find the association rules among time, space, disasters and fault facilities in the power system accident cases in extreme climate. That is very useful in power system fault analysis.


Author(s):  
Duangui Wang

Formulation of the problem. In the chamber-vocal genre, the composer exists in two images: he is both the interpreter of the poetic composition and the author of a new synthetic music and poetic composition. The experience of the style analysis of one of the best examples of Ukrainian vocal lyrics of the first third of the 20th century shows that the cycle op. 20 characterizes the mature style of the composer, which was formed, on the one hand, under the influence of European Romanticism. On the other hand, the essence of the Ukrainian “branch” of the Western European song-romance (“solo-singing”) is revealed by the prominent national song-romance intonation, filled with not only a romantic worldview, but also with some personal sincerity, chastity, intimate involvement with the great in depth and simplicity poetry line, read from the individual position of the musician. The paradox is as follows. Although Pushkin’s poetry is embodied in a “holistic adequacy” (A. Khutorskaya), and the composer found the fullest semantic analogue of the poetic source, however, in terms of translating the text into the Ukrainian language, the musical semantics changes its intonation immanence, which naturally leads to inconsistency of the listeners’ position and ideas about the style of Russian romance. We are dealing with inter-specific literary translation: Pushkin’s discourse creates the Ukrainian romance style and system of figurative thinking. The purpose of the article is to reveal the principle of re-semantization of the intonation-figurative concept of the vocal composition by V. Kosenko (in the context of translating Pushkin’s poetry into the Ukrainian language) in light of the theory of interspecific art translation. Analysis of recent publications on the topic. Among the most recent studies of Ukrainian musicology, one should point out the dissertation by G. Khafizova (Kyiv, 2017), in which the theory of modelling of the stylistic system of the vocal composition as an expression of Pushkin’s discourse is described. The basis for the further stylistic analysis of V. Kosenko’s compositions is the points from A. Hutorska’s candidate’s thesis; she develops the theory of interspecific art translation. The types of translation of poetry into music are classified according to two parameters. The exact translation creates integral adequacy, which involves the composer’s finding a maximally full semantic analogue of the poetic source. The free translation is characterized by compensatory, fragmentary, generalized-genre adequacy. Presenting the main material. The Zhitomir period for Viktor Kosenko was the time of the formation of his creative style. Alongside the lyrical imagery line, the composer acquired one more – dramatic, after his mother’s death. It is possible that the romances on the poems of A. Pushkin are more late reflection of this tragic experience (op. 20 was created in 1930). “I Loved You” opens the vocal cycle and has been dedicated by A. V. Kosenko. The short piano introduction contains the intonation emblem of the love-feeling wave. The form of the composition is a two part reprising (А А1) with the piano Introduction and Postlude. The semantic culmination is emphasized by the change of metro-rhythmic organization 5/4 (instead of 4) and the plastic phrase “as I wish, that the other will love you” sounding in the text. Due to these melodies (with national segments in melo-types, rhythm formulas and harmony) V. Kosenko should be considered as “Ukrainian Glinka”, the composer who introduced new forms and “figures” of the love language into the romantic “intonation dictionary”. In general, V. Kosenko’s solo-singing represents the Ukrainian analogue of Pushkin’s discourse – the theme of love. The melos of vocal piece “I Lived through My Desires” is remembered by the broad breath, bright expression of the syntactic deployment of emotion. On the background of bass ostinato, the song intonation acquires a noble courage. This solo-singing most intermediately appeal to the typical examples of the urban romance of Russian culture of the 19th century. “The Raven to the Raven” – a Scottish folk ballad in the translation by A. Pushkin. V. Kosenko as a profound psychologist, delicately transmits the techniques of versification, following each movement of a poetic phrase, builds stages of the musical drama by purely intonation means. The semantics of a death is embodied through the sound imaging of a black bird: a marching-like tempo and rhythm of the accompaniment, with a characteristic dotted pattern in a descending motion (like a raven is beating its wings). The middle section is dominated by a slow-motion perception of time space (Andante), meditative “freeze” (size 6/4). The melody contrasts with the previous section, its profile is built on the principle of descending move: from “h1” to “h” of the small octave (with a stop on S-harmony), which creates a psychologically immersed state, filled by premonition of an unexpected tragedy. In general, the Ukrainian melodic intonation intensified the tragic content of the ballad by Pushkin. The musical semantics of V. Kosenko’s romances is marked by the dependence on the romantic “musical vocabulary”, however, it is possible to indicate and national characteristics (ascending little-sixth and fifth intervals, which is filled with a gradual anti-movement; syllabic tonic versification, and other). Conclusion. The romances (“solo-singings”) by V. Kosenko belongs to the type of a free art translation with generalized-genre adequacy. There is a re-semantization of poetic images due to the national-mental intonation. Melos, rhythm, textural presentation (repetitions), stylization of different genre formulas testify to the rare beauty of Kosenko’s vocal style, spiritual strength and maturity of the master of Ukrainian vocal culture. Entering the “Slavic song area”, the style of Ukrainian romance, however, is differenced from the Russian and common European style system of figurative and intonation thinking (the picture of the world).


2021 ◽  
Author(s):  
Disha Bhange ◽  
Nityanand Prasad ◽  
Swati Singh ◽  
Harshit Kumar Prajapati ◽  
Shesh Prakash Maurya ◽  
...  

AbstractIn a multicentric, observational, investigator-blinded, and longitudinal clinical study of 764 ART-naïve subjects, we identified nine different promoter-variant strains of HIV-1 subtype C (HIV-1C) emerging in the Indian population, with some of these variants being reported for the first time. Unlike several previous studies, our work here focuses on the evolving viral regulatory elements, not coding sequences. The emerging viral strains contain additional copies of the existing transcription factor binding sites (TFBS), including TCF-1α/LEF-1, RBEIII, AP-1, and NF-κB, created by sequence duplication. The additional TFBS are genetically diverse and may blur the distinction between the modulatory region of the promoter and the viral enhancer. In a follow-up analysis, we found trends, but not significant associations between any specific variant promoter and prognostic markers, probably because the emerging viral strains might not have established mono infections yet. Illumina sequencing of four clinical samples containing a co-infection indicated the domination of one strain over the other and establishing a stable ratio with the second strain at the follow-up time-points. Since a single promoter regulates viral gene expression and constitutes the master regulatory circuit with Tat, the acquisition of additional and variant copies of the TFBS may significantly impact viral latency and latent reservoir characteristics. Further studies are urgently warranted to understand how the diverse TFBS profiles of the viral promoter may modulate the characteristics of the latent reservoir, especially following the initiation of antiretroviral therapy.Significance StatementA unique conglomeration of TFBS enables the HIV-1 promoter to accomplish two diametrically opposite functions – transcriptional activation and transcriptional silencing. The various phases of viral latency - establishment, maintenance, and reversal - collectively determine the replication fitness of individual viral strains. A profound variation in the TFBS composition of the viral promoter may significantly alter the viral latency properties and the latent reservoir characteristics. Although the duplication of certain TFBS remains a quality unique to HIV-1C, the high-level genetic recombination of HIV-1 may promote the transfer of such molecular properties to the other HIV-1 subtypes. The emergence of several promoter-variant viral strains may make the task of a ‘functional cure’ more challenging in HIV-1C.


Development ◽  
2002 ◽  
Vol 129 (10) ◽  
pp. 2339-2354 ◽  
Author(s):  
James M. McClintock ◽  
Mazen A. Kheirbek ◽  
Victoria E. Prince

We have used a morpholino-based knockdown approach to investigate the functions of a pair of zebrafish Hox gene duplicates, hoxb1a and hoxb1b, which are expressed during development of the hindbrain. We find that the zebrafish hoxb1 duplicates have equivalent functions to mouse Hoxb1 and its paralogue Hoxa1. Thus, we have revealed a ‘function shuffling’ among genes of paralogue group 1 during the evolution of vertebrates. Like mouse Hoxb1, zebrafish hoxb1a is required for migration of the VIIth cranial nerve branchiomotor neurons from their point of origin in hindbrain rhombomere 4 towards the posterior. By contrast, zebrafish hoxb1b, like mouse Hoxa1, is required for proper segmental organization of rhombomere 4 and the posterior hindbrain. Double knockdown experiments demonstrate that the zebrafish hoxb1 duplicates have partially redundant functions. However, using an RNA rescue approach, we reveal that these duplicated genes do not have interchangeable biochemical functions: only hoxb1a can properly pattern the VIIth cranial nerve. Despite this difference in protein function, we provide evidence that the hoxb1 duplicate genes were initially maintained in the genome because of complementary degenerative mutations in defined cis-regulatory elements.


Development ◽  
1992 ◽  
Vol 116 (2) ◽  
pp. 447-456 ◽  
Author(s):  
G. Tremml ◽  
M. Bienz

Extracellular signal proteins induce the homeotic gene labial (lab) to high levels of localised expression in the endoderm of Drosophila embryos. We aimed to identify cis-regulatory elements within the lab gene that respond to this induction by analysing the activity of stably integrated reporter gene constructs. Dissection of lab 5′ flanking sequences reveals two types of response elements. One of these mediates lab dependent activity, providing evidence that lab induction in the endoderm is autoregulatory. The other element, to a large extent independent of lab function, responds to decapentaplegic (dpp), a signal molecule related to mammalian TGF-beta. Our evidence suggests that lab induction in the endoderm reflects coordinate action of two distinct factors one of which may be lab protein itself, and another whose localised activity or expression in the midgut depends on the dpp signal.


DIALOGO ◽  
2021 ◽  
Vol 8 (1) ◽  
pp. 205-217
Author(s):  
Stephan A Schwartz

"This paper addresses the central idea of nonlocal consciousness: that all life is interconnected and interdependent, that we are part of a matrix of life, but even more fundamentally than spacetime itself arises from consciousness, not consciousness from spacetime. It is not a new idea. The excavation of burials dating to the Neolithic (≈ 10,200-2,000 BCE) has revealed that early humans had a sense of spirituality and some concept about the nature of human consciousness. It discusses the bargain made between the Roman Church, and the emerging discipline of science in the 16th century, one taking consciousness (packaged as “spirit”), the other spacetime, and how this led to physicalism taking root as a world view and becoming the prevailing materialist paradigm. It describes the emergence of a new paradigm that incorporates consciousness and lays out the four relevant descriptors helping to define what this new paradigm will look like. They are: • Only certain aspects of the mind are the result of physiologic processes. • Consciousness is causal, and physical reality is its manifestation. • All consciousnesses, regardless of their physical manifestations, are part of a network of life which they both inform and influence and are informed and influenced by; there is a passage back and forth between the individual and the collective. • Some aspects of consciousness are not limited by the time/space continuum and do not originate entirely within an organism’s neuroanatomy. "


1994 ◽  
Vol 14 (8) ◽  
pp. 5474-5486
Author(s):  
C A Dechesne ◽  
Q Wei ◽  
J Eldridge ◽  
L Gannoun-Zaki ◽  
P Millasseau ◽  
...  

Members of the MyoD family of gene-regulatory proteins (MyoD, myogenin, myf5, and MRF4) have all been shown not only to regulate the transcription of numerous muscle-specific genes but also to positively autoregulate and cross activate each other's transcription. In the case of muscle-specific genes, this transcriptional regulation can often be correlated with the presence of a DNA consensus in the regulatory region CANNTG, known as an E box. Little is known about the regulatory interactions of the myogenic factors themselves; however, these interactions are thought to be important for the activation and maintenance of the muscle phenotype. We have identified the minimal region in the chicken MyoD (CMD1) promoter necessary for muscle-specific transcription in primary cultures of embryonic chicken skeletal muscle. The CMD1 promoter is silent in primary chick fibroblast cultures and in muscle cell cultures treated with the thymidine analog bromodeoxyuridine. However, CMD1 and chicken myogenin, as well as, to a lesser degree, chicken Myf5 and MRF4, expressed in trans can activate transcription from the minimal CMD1 promoter in these primary fibroblast cultures. Here we show that the CMD1 promoter contains numerous E-box binding sites for CMD1 and the other myogenic factors, as well as a MEF-2 binding site. Surprisingly, neither muscle-specific and the other myogenic factors, as well as a MEF-2 binding site. Surprisingly, neither muscle-specific expression, autoregulation, or cross activation depends upon the presence of of these E-box or MEF-2 binding sites in the CMD1 promoter. These results demonstrate that the autoregulation and cross activation of the chicken MyoD promoter through the putative direct binding of the myogenic basic helix-loop-helix regulatory factors is mediated through an indirect pathway that involves unidentified regulatory elements and/or ancillary factors.


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