Empty Site Models for Heap Formation in Vertically Vibrating Grains

1999 ◽  
Vol 83 (19) ◽  
pp. 3832-3835 ◽  
Author(s):  
L. C. Jia ◽  
Pik-Yin Lai ◽  
C. K. Chan
Keyword(s):  
Empty Site

scholarly journals Extensive, Nonrandom Diversity of Excision Footprints Generated by Ds-Like Transposon Ascot-1Suggests New Parallels with V(D)J Recombination

1998 ◽  
Vol 18 (7) ◽  
pp. 4337-4346 ◽  
Author(s):  
Vincent Colot ◽  
Vicki Haedens ◽  
Jean-Luc Rossignol
Keyword(s):  
Extensive Study ◽  
Empty Site ◽  
Site Factors ◽  
Original Sequence ◽  
Ascobolus Immersus ◽  
High Degree ◽  
Hairpin Formation ◽  
Processing Steps ◽  
Color Gene

ABSTRACT Upon insertion, transposable elements can disrupt or alter gene function in various ways. Transposons moving through a cut-and-paste mechanism are in addition often mutagenic when excising because repair of the empty site seldom restores the original sequence. The characterization of numerous excision events in many eukaryotes indicates that transposon excision from a given site can generate a high degree of DNA sequence and phenotypic variation. Whether such variation is generated randomly remains largely to be determined. To this end, we have exploited a well-characterized system of genetic instability in the fungus Ascobolus immersus to perform an extensive study of excision events. We show that this system, which produces many phenotypically and genetically distinct derivatives, results from the excision of a novel Ds-like transposon,Ascot-1, from the spore color gene b2. A unique set of 48 molecularly distinct excision products were readily identified from a representative sample of excision derivatives. Products varied in their frequency of occurrence over 4 orders of magnitude, yet most showed small palindromic nucleotide additions. Based on these and other observations, compelling evidence was obtained for intermediate hairpin formation during the excision reaction and for strong biases in the subsequent processing steps at the empty site. Factors likely to be involved in these biases suggest new parallels between the excision reaction performed by transposons of thehAT family and V(D)J recombination. An evaluation of the contribution of small palindromic nucleotide additions produced by transposon excision to the spectrum of spontaneous mutations is also presented.

scholarly journals Human DNA Telomeres in Presence of Oxidative Lesions: The Crucial Role of Electrostatic Interactions on the Stability of Guanine Quadruplexes

Antioxidants ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. 337 ◽  
Author(s):  
Hognon ◽  
Gebus ◽  
Barone ◽  
Monari
Keyword(s):  
Electrostatic Interactions ◽  
Empty Site ◽  
Quadruplex Structure ◽  
Abasic Sites ◽  
Human Dna ◽  
Guanine Quadruplex ◽  
Guanine Base ◽  
The Stability ◽  
Dynamics Simulations

By using all atom molecular dynamics simulations, we studied the behavior of human DNA telomere sequences in guanine quadruplex (G4) conformation and in the presence of oxidative lesions, namely abasic sites. In particular, we evidenced that while removing one guanine base induces a significant alteration and destabilization of the involved leaflet, human telomere oligomers tend, in most cases, to maintain at least a partial quadruplex structure, eventually by replacing the empty site with undamaged guanines of different leaflets. This study shows that (i) the disruption of the quadruplex leaflets induces the release of at least one of the potassium cations embedded in the quadruplex channel and that (ii) the electrostatic interactions of the DNA sequence with the aforementioned cations are fundamental to the maintenance of the global quadruplex structure.

scholarly journals Helicobacter pylori cag pathogenicity island genotype diversity within the gastric niche of a single host

2007 ◽  
Vol 56 (5) ◽  
pp. 664-669 ◽  
Author(s):  
Mario José Matteo ◽  
Gabriela Granados ◽  
Cecilia Valeria Pérez ◽  
Martín Olmos ◽  
Cristian Sanchez ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Clinical Presentation ◽  
Random Amplified Polymorphic Dna ◽  
Positive Culture ◽  
Pathogenicity Island ◽  
Empty Site ◽  
Multiple Biopsies ◽  
Single Host ◽  
Dna Pcr ◽  
Positive Half

cag pathogenicity island (PAI) integrity was investigated in isolates from multiple biopsies recovered from 40 patients in an attempt to determine the co-existence of a varying cagPAI-positive to cagPAI-negative ratio in a single host. Six biopsies were obtained from each patient during the same endoscopic session. cagPAI analysis included amplification of seven loci (cagA, cagE, cagG, cagM, cagT, HP0527 and HP0524) and the left end of cagII (LEC). Absence of the island was confirmed by empty-site PCR. lspA-glmM RFLP and random amplified polymorphic DNA PCR were used for strain delineation. The number of biopsies with Helicobacter pylori-positive culture ranged from three to six per patient and a total of 218 isolates were recovered. Mixed infection was only found in two patients. Nearly one-third of the 40 patients harboured isolates with an intact cagPAI in all niches, another third of the isolates were empty-site-positive in all niches, whilst the remaining third of the isolates had a disrupted cagPAI in all or at least one of the niches. Co-existence of variants of the same strain with different cagPAI genotypes was observed in one-quarter of patients. The variations in cagPAI genotype included co-existence of: diverse cagPAI deletions in different niches, variants with intact and with partially deleted islands, variants with empty-site-positive and with partially deleted cagPAIs, and variants with an intact cagPAI and with empty-site-positive. Half of the patients with different cagPAI genotypes harboured an intact cagPAI in at least one niche. Co-existence of diverse genotypes of putative virulence factors in a single host must be considered when drawing a correlation with clinical presentation.

Tacitus's Dangerous Word

2004 ◽  
Vol 23 (1) ◽  
pp. 33-61 ◽  
Author(s):  
Holly Haynes
Keyword(s):  
Public Affairs ◽  
The Political ◽  
Empty Site ◽  
Political Unconscious ◽  
The Public ◽  
The Past ◽  
The Republic

AbstractThe fact that vocabulum appears with far more frequency in Tacitus' texts than in any other author except for the encyclopaedists argues for his idiosyncratic usage of the term. This article argues that imperial discourse, nearly identical in structure and expression to that of the Republic but divorced from Republican connotations, provided an empty site where Roman fantasies of self-definition took strong hold, and that Tacitus uses vocabulum to indicate words and concepts that illustrate this process, particularly with reference to representations of the foreign and the past. Such a discourse was congenial for the concentration of power in the hands of one person, as it no longer expressed the conflicting desires of a community engaged in public affairs, but collectivized the public desire for an image of Roman superiority. Thus Germany and the old Republican past were easily mythologized as what Rome desired to be, but feared it was not. Tacitus' use of vocabulum highlights the words in imperial discourse that betray the gap in the political unconscious between Romans' idea of themselves as masters of the Empire and as slaves to one ruler. Nor does he position himself as an outside observer of this process, but creates an experience of it for the reader through gaps and inconsistencies within his narrative.

EXCITONIC MECHANISM FOR SUPERCONDUCTIVITY IN DOPED MOTT INSULATOR

1992 ◽  
Vol 06 (07) ◽  
pp. 383-390 ◽  
Author(s):  
MICHEL CYROT
Keyword(s):  
Strong Interaction ◽  
Mott Insulator ◽  
Bound State ◽  
Empty Site ◽  
Small Energy ◽  
Hartree Fock ◽  
Doped Mott Insulator ◽  
The Creation ◽  
Excitonic Mechanism

We argue that when a Mott insulator is doped, it exists a range of concentration where two kinds of excitations coexist. Besides those of the usual Hartree-Fock metal, metallic excitons of very small energy persist. These excitons stems from the creation of an empty site surrounded by a virtual bound state in the band. Due to the strong interaction between electrons and metallic excitons, excitonic superconductivity is favoured.

THE INFLUENCE OF COADSORBATES (K, O) ON THE AUTOCATALYTIC DECOMPOSITION OF ACETIC ACID ON Rh{111}

1994 ◽  
Vol 01 (04) ◽  
pp. 553-555 ◽  
Author(s):  
D.C. PAPAGEORGOPOULOS ◽  
G. HOOGERS ◽  
D.A. KING
Keyword(s):  
Acetic Acid ◽  
Room Temperature ◽  
Autocatalytic Decomposition ◽  
Empty Site ◽  
Autocatalytic Mechanism ◽  
Intermediate Effect

The autocatalytic decomposition of acetic acid has been studied with TPD on the Rh{111} surface with and without the presence of coadsorbates. Sharp H2 and CO 2 desorption peaks indicating autocatalytic processes are produced after saturating the surface with acetate, and also after coadsorption of oxygen and potassium at room temperature. Oxygen is found to stabilize the acetate; potassiun destabilizes the acetate, and O/K mixtures have an intermediate effect. The results are discussed in terms of a simple empty-site-creation autocatalytic mechanism for systems in which the surface is initially fully saturated with adsorbate species.

scholarly journals A molecular marker set combining a retrotransposon insertion and SSR polymorphisms is useful for assessing diversity in Vitis

OENO One ◽  
2021 ◽  
Vol 55 (2) ◽  
pp. 403-414
Author(s):  
Frederique Pelsy ◽  
Lucie Bevilacqua ◽  
Sophie Blanc ◽  
Didier Merdinoglu
Keyword(s):  
Molecular Markers ◽  
Molecular Marker ◽  
Phylogenetic Relationships ◽  
Genetic Material ◽  
Dna Polymorphisms ◽  
Heterozygous State ◽  
Empty Site ◽  
Microsatellite Sequence ◽  
Vitis Species ◽  
Ssr Polymorphism

Molecular markers, based on DNA polymorphisms, are useful tools for identifying individuals, establishing phylogenetic relationships, managing collections of genetic material or assisting breeding. In the present study, we developed a marker set to differentiate Vitis species, grapevine varieties or clones belonging to the same variety. This novel marker set combines, in four PCR amplifications, the presence/absence of a remarkable retrotransposon, Tvv1-Δ3460, inserted at its single locus and the SSR polymorphism present within its two LTRs. By studying a collection of Vitaceaeaccessions, we showed the prevalence of two allelic forms of Tvv1-Δ3460 - one of which was partially truncated - in Vitis species. Out of the twenty-five studied Vitis species, the insertion of a Tvv1-Δ3460 element was detected in twenty, including Vitis vinifera. The homozygous vs heterozygous state of the element insertion was determined by amplifying the empty site. Additionally, each Tvv1-Δ3460 LTRs included a microsatellite sequence useful for designing markers based on LTR length. The LTR-SSR markers distinguished most of the fifty-two cultivars and revealed polymorphism within five of the seven varieties studied.

There was once an empty site

2020 ◽  
Vol 24 (2) ◽  
pp. 129-140
Author(s):  
Catalina Mejía Moreno
Keyword(s):  
Empty Site ◽  
Mies Van Der Rohe

This article unveils and discusses a series of unknown photographs of the empty site in which Mies and Lilly Reich's 1929 German Pavilion in Barcelona had been built and dismantled, and shot by Ludwig Glaeser, curator of the Mies van der Rohe Archive at MoMA in 1979. It suggests that more than the manifestation of a desire to rematerialise the building through the agency of photography, Glaeser's photographs are, photographs of dust, but more importantly, a manifestation of the possibility of re-enacting the widely known 1929 Berliner Bild-Bericht photographs.

scholarly journals Atomtronics with holes: Coherent transport of an empty site in a triple-well potential

2010 ◽  
Vol 82 (1) ◽  
Author(s):  
A. Benseny ◽  
S. Fernández-Vidal ◽  
J. Bagudà ◽  
R. Corbalán ◽  
A. Picón ◽  
...  
Keyword(s):  
Empty Site ◽  
Coherent Transport
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