Identification of a set of widely expressed genes in grape (Vitis vinifera L.) and its functional characterisation: a multi-evidence based study

Quantitative gene expression data analysis requires efficient normalization to be really informative: as a consequence reference genes that are stably expressed in tested vs. control samples are used for results standardization. The identification of tissue-wide-expressed genes makes it easier to highlight the best set of candidate internal controls. While tissue-specific genes are often regulated by microRNA, housekeeping genes, being involved in cell maintenance and thus required in all miRNA expressing cells are not expected to be microRNA targets. In this work we have identified a set of tissue-wide expressed genes in grape which has then been functionally characterised and scanned for the presence vs. absence of putative miRNA target sites. The gene list obtained by this multi-evidence based procedure can be helpful to identify appropriate references in grape.

Energy relaxation in disordered charge and spin density waves

We investigate collective effects in the strong pinning model of disordered charge and spin density waves (CDWs and SDWs) in connection with heat relaxation experiments. We discuss the classical and quantum limits that contribute to two distinct contribution to the specific heat (a $C_v \sim T^{-2}$ contribution and a $C_v \sim T^{\alpha}$ contribution respectively), with two different types of disorder (strong pinning versus substitutional impurities). From the calculation of the two level system energy splitting distribution in the classical limit we find no slow relaxation in the commensurate case and a broad spectrum of relaxation times in the incommensurate case. In the commensurate case quantum effects restore a non vanishing energy relaxation, and generate stronger disorder effects in incommensurate systems. For substitutional disorder we obtain Friedel oscillations of bound states close to the Fermi energy. With negligible interchain couplings this explains the power-law specific heat $C_v \sim T^{\alpha}$ observed in experiments on CDWs and SDWs combined to the power-law susceptibility $\chi(T)\sim T^{-1+\alpha}$ observed in the CDW o-TaS$_3$.Comment: 13 pages, 10 figures, improvements in the presentatio

Wood chemotaxonomy via ESI-MS profiles of phytochemical markers: the challenging case of african versus brazilian mahogany woods

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)The harvesting of Brazilian mahogany (Swietenia macrophylla) is a main cause of the Brazilian Amazon deforestation and has been therefore prohibited. African mahogany (Khaya ivorensis) was then introduced for Amazon reforestation and the commercialization of such wood is legal, thus creating a challenging problem for wood certification. Herein we report that a wood chemotaxonomic method based on distinct profiles of phytochemical markers is able to promptly characterize both the native and foreign mahogany species. This challenging task has been performed via a simple, fast and unambiguous methodology using direct electrospray ionization mass spectrometry (ESI-MS) analysis of a simple methanolic extract of a tiny wood chip. Typical limonoids such as khivorin, khayanolide A and mexicanolide for African mahogany and phragmalin-type limonoids for the native Brazilian species, as well as distinct polyphenols such as catechin derivatives and cinchonain, form the characteristic phytochemical marker pools for both species. This rapid methodology could therefore be used to monitor legal and illegal mahogany tree harvesting, and hence to control Amazon deforestation. It could also be applied to create a wood certification program for African and Brazilian mahogany trees, as well as for wood certification in general.The harvesting of Brazilian mahogany (Swietenia macrophylla) is a main cause of the Brazilian Amazon deforestation and has been therefore prohibited. African mahogany (Khaya ivorensis) was then introduced for Amazon reforestation and the commercialization72085768583FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOFINEP - FINANCIADORA DE ESTUDOS E PROJETOSFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)sem informaçãosem informaçãosem informaçã

Memory Effects in Granular Material

We present a combined experimental and theoretical study of memory effects in vibration-induced compaction of granular materials. In particular, the response of the system to an abrupt change in shaking intensity is measured. At short times after the perturbation a granular analog of aging in glasses is observed. Using a simple two-state model, we are able to explain this short-time response. We also discuss the possibility for the system to obey an approximate pseudo-fluctuation-dissipation theorem relationship and relate our work to earlier experimental and theoretical studies of the problem.Comment: 5 pages, 4 figures, reference list change

Cognitive reserve in granulin-related frontotemporal dementia: from preclinical to clinical stages

OBJECTIVE Consistent with the cognitive reserve hypothesis, higher education and occupation attainments may help persons with neurodegenerative dementias to better withstand neuropathology before developing cognitive impairment. We tested here the cognitive reserve hypothesis in patients with frontotemporal dementia (FTD), with or without pathogenetic granulin mutations (GRN+ and GRN-), and in presymptomatic GRN mutation carriers (aGRN+). METHODS Education and occupation attainments were assessed and combined to define Reserve Index (RI) in 32 FTD patients, i.e. 12 GRN+ and 20 GRN-, and in 17 aGRN+. Changes in functional connectivity were estimated by resting state fMRI, focusing on the salience network (SN), executive network (EN) and bilateral frontoparietal networks (FPNs). Cognitive status was measured by FTD-modified Clinical Dementia Rating Scale. RESULTS In FTD patients higher level of premorbid cognitive reserve was associated with reduced connectivity within the SN and the EN. EN was more involved in FTD patients without GRN mutations, while SN was more affected in GRN pathology. In aGRN+, cognitive reserve was associated with reduced SN. CONCLUSIONS This study suggests that cognitive reserve modulates functional connectivity in patients with FTD, even in monogenic disease. In GRN inherited FTD, cognitive reserve mechanisms operate even in presymptomatic to clinical stages

Mean-field theory of temperature cycling experiments in spin-glasses

We study analytically the effect of temperature cyclings in mean-field spin-glasses. In accordance with real experiments, we obtain a strong reinitialization of the dynamics on decreasing the temperature combined with memory effects when the original high temperature is restored. The same calculation applied to mean-field models of structural glasses shows no such reinitialization, again in accordance with experiments. In this context, we derive some relations between experimentally accessible quantities and propose new experimental protocols. Finally, we briefly discuss the effect of field cyclings during isothermal aging.Comment: Some misprints corrected, references updated, final version to apper in PR

Apraxia and motor dysfunction in corticobasal syndrome

Background: Corticobasal syndrome (CBS) is characterized by multifaceted motor system dysfunction and cognitive disturbance; distinctive clinical features include limb apraxia and visuospatial dysfunction. Transcranial magnetic stimulation (TMS) has been used to study motor system dysfunction in CBS, but the relationship of TMS parameters to clinical features has not been studied. The present study explored several hypotheses; firstly, that limb apraxia may be partly due to visuospatial impairment in CBS. Secondly, that motor system dysfunction can be demonstrated in CBS, using threshold-tracking TMS, and is linked to limb apraxia. Finally, that atrophy of the primary motor cortex, studied using voxel-based morphometry analysis (VBM), is associated with motor system dysfunction and limb apraxia in CBS.   Methods: Imitation of meaningful and meaningless hand gestures was graded to assess limb apraxia, while cognitive performance was assessed using the Addenbrooke's Cognitive Examination - Revised (ACE-R), with particular emphasis placed on the visuospatial subtask. Patients underwent TMS, to assess cortical function, and VBM.   Results: In total, 17 patients with CBS (7 male, 10 female; mean age 64.4+/2 6.6 years) were studied and compared to 17 matched control subjects. Of the CBS patients, 23.5% had a relatively inexcitable motor cortex, with evidence of cortical dysfunction in the remaining 76.5% patients. Reduced resting motor threshold, and visuospatial performance, correlated with limb apraxia. Patients with a resting motor threshold <50% performed significantly worse on the visuospatial sub-task of the ACE-R than other CBS patients. Cortical function correlated with atrophy of the primary and pre-motor cortices, and the thalamus, while apraxia correlated with atrophy of the pre-motor and parietal cortices.   Conclusions: Cortical dysfunction appears to underlie the core clinical features of CBS, and is associated with atrophy of the primary motor and pre-motor cortices, as well as the thalamus, while apraxia correlates with pre-motor and parietal atrophy

Glassy systems under time-dependent driving forces: application to slow granular rheology

We study the dynamics of a glassy model with infinite range interactions externally driven by an oscillatory force. We find a well-defined transition in the (Temperature-Amplitude-Frequency) phase diagram between (i) a `glassy' state characterized by the slow relaxation of one-time quantities, aging in two-time quantities and a modification of the equilibrium fluctuation-dissipation relation; and (ii) a `liquid' state with a finite relaxation time. In the glassy phase, the degrees of freedom governing the slow relaxation are thermalized to an effective temperature. Using Monte-Carlo simulations, we investigate the effect of trapping regions in phase space on the driven dynamics. We find that it alternates between periods of rapid motion and periods of trapping. These results confirm the strong analogies between the slow granular rheology and the dynamics of glasses. They also provide a theoretical underpinning to earlier attempts to present a thermodynamic description of moderately driven granular materials.Comment: Version accepted for publication - Physical Review