DNA loops and semicatenated DNA junctions

BACKGROUND: Alternative DNA conformations are of particular interest as potential signals to mark important sites on the genome. The structural variability of CA microsatellites is particularly pronounced; these are repetitive poly(CA) · poly(TG) DNA sequences spread in all eukaryotic genomes as tracts of up to 60 base pairs long. Many in vitro studies have shown that the structure of poly(CA) · poly(TG) can vary markedly from the classical right handed DNA double helix and adopt diverse alternative conformations. Here we have studied the mechanism of formation and the structure of an alternative DNA structure, named Form X, which was observed previously by polyacrylamide gel electrophoresis of DNA fragments containing a tract of the CA microsatellite poly(CA) · poly(TG) but had not yet been characterized. RESULTS: Formation of Form X was found to occur upon reassociation of the strands of a DNA fragment containing a tract of poly(CA) · poly(TG), in a process strongly stimulated by the nuclear proteins HMG1 and HMG2. By inserting Form X into DNA minicircles, we show that the DNA strands do not run fully side by side but instead form a DNA knot. When present in a closed DNA molecule, Form X becomes resistant to heating to 100°C and to alkaline pH. CONCLUSIONS: Our data strongly support a model of Form X consisting in a DNA loop at the base of which the two DNA duplexes cross, with one of the strands of one duplex passing between the strands of the other duplex, and reciprocally, to form a semicatenated DNA junction also called a DNA hemicatenane

Avoiding adsorption of DNA to polypropylene tubes and denaturation of short DNA fragments.

Two problems can arise when working with small quantities of DNA in polypropylene tubes: first, significant amounts of DNA can become lost by sticking to the tube walls; second, short DNA fragments tend to denature when binding to polypropylene. In addition, DNA also tends to denature upon dehydration. We have found that a simple way to solve these problems is by using polyallomer tubes instead of polypropylene and by avoiding certain salts, such as sodium acetate, when drying DNA

High affinity binding of proteins HMG1 and HMG2 to semicatenated DNA loops

BACKGROUND: Proteins HMG1 and HMG2 are two of the most abundant non histone proteins in the nucleus of mammalian cells, and contain a domain of homology with many proteins implicated in the control of development, such as the sex-determination factor Sry and the Sox family of proteins. In vitro studies of interactions of HMG1/2 with DNA have shown that these proteins can bind to many unusual DNA structures, in particular to four-way junctions, with binding affinities of 10(7) to 10(9) M(-1). RESULTS: Here we show that HMG1 and HMG2 bind with a much higher affinity, at least 4 orders of magnitude higher, to a new structure, Form X, which consists of a DNA loop closed at its base by a semicatenated DNA junction, forming a DNA hemicatenane. The binding constant of HMG1 to Form X is higher than 5 × 10(12) M(-1), and the half-life of the complex is longer than one hour in vitro. CONCLUSIONS: Of all DNA structures described so far with which HMG1 and HMG2 interact, we have found that Form X, a DNA loop with a semicatenated DNA junction at its base, is the structure with the highest affinity by more than 4 orders of magnitude. This suggests that, if similar structures exist in the cell nucleus, one of the functions of these proteins might be linked to the remarkable property of DNA hemicatenanes to associate two distant regions of the genome in a stable but reversible manner

Writing Disability in ADHD Children

The psychological examination aims at objectifying the key symptoms of hyperactivity, i.e. attention and executive function disorders (in short, activation-inhibition control). The files of 237 patients from our consultations, aged between 5 and 17 years old and examined between 2004 and 2016, are analyzed retrospectively. Of whom 40 cases show the typical ADHD syndrome, mixed presentation, according to DSM-5 criteria. These ADHD children and adolescents show not only a characteristic impulsivity on computerized attention tests, but also a deficit in the acquisition of writing, an early manifestation of their neurodevelopmental disorders. This association correctly classifies 82.4% of hyperactives and controls, a strong effect given the difficult diagnosis of ADHD syndrome

J'apprends, donc je suis. I learn, therefore I am

J’APPRENDS, DONC JE SUIS. Résumé Le psychologue qui travaille dans les écoles voit des enfants et des adolescents en conflit avec eux-mêmes, avec l’école, ou avec l’apprendre. Le présent chapitre montre que dans tous les cas, il s’agit d’un conflit d’identité, celle de l’apprenant. A l’aide de trois exemples de dyscalculie développementale, nous montrons que la plupart des troubles spécifiques de l’apprentissage a ses origines dans le développement préscolaire de l’enfant et entraîne subséquemment certaines comorbidités. Une des clés de l’apprendre est le développement des fonctions exécutives qui permet d’apprendre à apprendre : nous montrons son rôle dans le développement de l’identité de l’écolier et dans la construction de sa personnalité. La vision de l’écolier différent s’en trouve changée. Il est un « apprenant autrement ». Cette perspective relativise le rôle des acteurs de l’éducation, élèves, parents, enseignants, avec leurs méthodes, et met en avant les « pourquoi et comment je progresse » dans la quête de l’apprenant. Mots clés Neuropsychologie du développement, apprentissage, apprendre, troubles spécifiques de l’apprentissage, dyscalculies, DYS, fonctions exécutives. I LEARN, THEREFORE I AM Summary School psychologists care of children and adolescents who live conflicts with themselves, with the school and with the challenge to learn. The present chapter shows that we actually deal with an identity problem, that of the learner. We comment on three cases of developmental dyscalculia which illustrate the history of preschool language, motor and spatial disorders and which lead to subsequent comorbidities. One major key of the learning process is, we think, the progressive role of the executive functions that motivate learning and contribute the the child’s personality development. Therefore the learning disabled reveals her/himself as a child who learns differently. « Why and how do I learn » participate to the construction of the learner’s self. Educative roles by parents and teachers with their didactics, if they exist, appear as of relative importance in comparison with this quest from the part of the learner. Key words Child neuropsychology, childhood learning, specific learning disabilities, developmental dyscalculia, executive functions

Genetic parameters of beef traits of Limousin and Charolais progeny-tested AI sires

Sire selection efficiency depends on the knowledge of accurate genetic parameters. In France, artificial insemination (AI) sires are selected according to their own performances and those of their progeny, which are both recorded in test stations. Genetic parameters among progeny traits were estimated using multi-trait REML ( restricted estimation of maximum likelihood) analyses in Charolais and Limousin breeds. The expected decrease in genetic variability algebraically calculated among progeny traits due to the selection of sires was not observed. This selection was not a strict truncation. Heritabilities of traits measured on progeny are moderate for growth traits, morphology and live fatness scores (from 0.14 to 0.38) and slightly higher for dressing percentage and carcass fatness score (0.50 and 0.44, respectively). Genetic correlations among progeny traits depended on traits, selection programme and breed. Carcass weight and morphology were highly genetically linked to corresponding live traits (live weight and conformation, respectively). They can, therefore, be easily improved through indirect selection in contrast to carcass fatness which has only a small genetic correlation with live traits

Hypothalamic ghrelin treatment modulates NPY- but not CRH-ergic activity in adrenalectomized rats subjected to food restriction: Evidence of a novel hypothalamic ghrelin effect

It has been proposed that ghrelin induces food intake by a mechanism due to the stimulation of hypothalamic NPY-ergic activity. It is recognized that bilateral adrenalectomy (ADX) enhances hypothalamic CRH-ergic function and reduces appetite. Thus, the aim of the present study was to test whether, icv-administered, ghrelin modulates NPY- and CRH-ergic functions after food restriction (FR) and glucocorticoid deprivation. For this purpose; 1 μg ghrelin was administered icv to ad libitum (AL) eating and to corticosterone (B)-depleted (ADX) and- replete (sham and ADX+B) male animals habituated, for 15 d, to FR. Food intake, hypothalamic function, and peripheral ghrelin, ACTH, and B concentrations were evaluated 2 h after ghrelin administration. Results indicate that while icv ghrelin treatment stimulated 2-h food intake in AL rats, it failed to do so in sham- and ADX+B-FR animals; moreover, 2-h food intake was inhibited by icv ghrelin treatment in ADX-FR rats. Regarding peripheral hormone levels: (a) basal circulating ghrelin levels, already enhanced (vs AL rats) by FR, significantly increased 2 h after icv ghrelin treatment in AL and sham-FR rats; (b) central ghrelin treatment stimulated ACTH secretion in circulation of AL and glucocorticoid-replete-FR rats; and (c) B circulating levels remained unchanged after ghrelin treatment, although they were in relation to the food intake condition of rats. Finally, hypothalamic NPY mRNA expression was enhanced by FR and, in response to icv ghrelin treatment, it decreased in ADX-FR rats only. ADX-enhanced hypothalamic CRH mRNA levels were reduced by ghrelin icv administration only when antimals received B replacement therapy. Our data indicate an inhibitory effect of hypothalamic ghrelin on NPY-ergic activity in FR rats lacking endogenous glucocorticoi

Acute Effects of TiO2 Nanomaterials on the Viability and Taxonomic Composition of Aquatic Bacterial Communities Assessed via High-Throughput Screening and Next Generation Sequencing

The nanotechnology industry is growing rapidly, leading to concerns about the potential ecological consequences of the release of engineered nanomaterials (ENMs) to the environment. One challenge of assessing the ecological risks of ENMs is the incredible diversity of ENMs currently available and the rapid pace at which new ENMs are being developed. High-throughput screening (HTS) is a popular approach to assessing ENM cytotoxicity that offers the opportunity to rapidly test in parallel a wide range of ENMs at multiple concentrations. However, current HTS approaches generally test one cell type at a time, which limits their ability to predict responses of complex microbial communities. In this study toxicity screening via a HTS platform was used in combination with next generation sequencing (NGS) to assess responses of bacterial communities from two aquatic habitats, Lake Michigan (LM) and the Chicago River (CR), to short-term exposure in their native waters to several commercial TiO2 nanomaterials under simulated solar irradiation. Results demonstrate that bacterial communities from LM and CR differed in their sensitivity to nano-TiO2, with the community from CR being more resistant. NGS analysis revealed that the composition of the bacterial communities from LM and CR were significantly altered by exposure to nano-TiO2, including decreases in overall bacterial diversity, decreases in the relative abundance of Actinomycetales, Sphingobacteriales, Limnohabitans, and Flavobacterium, and a significant increase in Limnobacter. These results suggest that the release of nano-TiO2 to the environment has the potential to alter the composition of aquatic bacterial communities, which could have implications for the stability and function of aquatic ecosystems. The novel combination of HTS and NGS described in this study represents a major advance over current methods for assessing ENM ecotoxicity because the relative toxicities of multiple ENMs to thousands of naturally occurring bacterial species can be assessed simultaneously under environmentally relevant conditions

Senescence in natural populations of animals:Widespread evidence and its implications for bio-gerontology

That senescence is rarely, if ever, observed in natural populations is an oft-quoted fallacy within bio-gerontology. We identify the roots of this fallacy in the otherwise seminal works of Medawar and Comfort, and explain that under antagonistic pleiotropy or disposable soma explanations for the evolution of senescence there is no reason why senescence cannot evolve to be manifest within the life expectancies of wild organisms. The recent emergence of long-term field studies presents irrefutable evidence that senescence is commonly detected in nature. We found such evidence in 175 different animal species from 340 separate studies. Although the bulk of this evidence comes from birds and mammals, we also found evidence for senescence in other vertebrates and insects. We describe how high-quality longitudinal field data allow us to test evolutionary explanations for differences in senescence between the sexes and among traits and individuals. Recent studies indicate that genes, prior environment and investment in growth and reproduction influence aging rates in the wild. We argue that – with the fallacy that wild animals do not senesce finally dead and buried – collaborations between bio-gerontologists and field biologists can begin to test the ecological generality of purportedly ‘public’ mechanisms regulating aging in laboratory models