Folding and cytoplasm viscoelasticity contribute jointly to chromosome dynamics

The chromosome is a key player of cell physiology, and its dynamics provides valuable information about its physical organization. In both prokaryotes and eukaryotes, the short-time motion of chromosomal loci has been described as a Rouse model in a simple or viscoelastic medium. However, little emphasis has been put on the role played by the folded organization of chromosomes on the local dynamics. Clearly, stress-propagation, and thus dynamics, must be affected by such organization, but a theory allowing to extract such information from data, e.g.\ of two-point correlations, is lacking. Here, we describe a theoretical framework able to answer this general polymer dynamics question, and we provide a general scaling analysis of the stress-propagation time between two loci at a given arclength distance along the chromosomal coordinate. The results suggest a precise way to detect folding information from the dynamical coupling of chromosome segments. Additionally, we realize this framework in a specific theoretical model of a polymer with variable-range interactions in a viscoelastic medium characterized by a tunable scaling exponent, where we derive analytical estimates of the correlation functions.Comment: 14 pages including supplementary material

Intrinsic dimension estimation for locally undersampled data

Identifying the minimal number of parameters needed to describe a dataset is a challenging problem known in the literature as intrinsic dimension estimation. All the existing intrinsic dimension estimators are not reliable whenever the dataset is locally undersampled, and this is at the core of the so called curse of dimensionality. Here we introduce a new intrinsic dimension estimator that leverages on simple properties of the tangent space of a manifold and extends the usual correlation integral estimator to alleviate the extreme undersampling problem. Based on this insight, we explore a multiscale generalization of the algorithm that is capable of (i) identifying multiple dimensionalities in a dataset, and (ii) providing accurate estimates of the intrinsic dimension of extremely curved manifolds. We test the method on manifolds generated from global transformations of high-contrast images, relevant for invariant object recognition and considered a challenge for state-of-the-art intrinsic dimension estimators

Preface: Bioplasmas and plasmas with liquids

The Bioplasma and Plasmas with Liquids joint conference of the COST Actions TD1208 Electrical discharges with liquids for future applications and MP1101 Biomedical applications of atmospheric pressure plasma technology was held in Bertinoro (Italy) on September 13-16, 2015. The purpose of the Bioplasma and Plasmas with Liquids joint conference was to bring together researchers of different fields, and to establish an open forum for presentation and discussion of the latest advances in the fields of electrical discharges with liquids and plasma medicine, by bridging the scientific communities associated with the COST Actions TD1208 Electrical discharges with liquids for future applications and MP1101 Biomedical applications of atmospheric pressure plasma technology

Sensing of gaseous malodors characteristic of landfills and waste treatment plants

Abstract. We approached the problem of sensing gaseous pollutants and malodors originating as a result of decomposition of organic compounds via chemoresistive sensors. A set of four screen-printed films based on two types of mixed tin and titanium oxides, mixed tungsten and tin oxides, and zinc oxide has been tested vs. the main gaseous components of malodors. N-butanol was also considered because of its importance as a reference gas in the odorimetric intensity scale. We found that, under proper working conditions, the films can sensitively detect such gases either in dry or in wet environments, within the range of concentrations of interest for their monitoring. We also demonstrated that the array is robust under solicitation by harmful interference gases such as CO, C6H6, NO2 and NO

Induction of resistance and enhancing agronomic performance in grapevines under greenhouse and in open fields by applications of plasma activated water

The exposure of water to a cold atmospheric pressure plasma (CAP) enables the production of plasma activated water (PAW), having high content of reactive species, whose applications were tested on grapevine plants, both in greenhouse and in vineyard conditions. Two different CAPs were used for PAW production, evaluating their effectiveness as a possible mean to control plant diseases. Grapevines infected with yellows associated with the presence of phytoplasmas were treated evaluating qualitative and quantitative yield parameters, phytoplasma presence, and gene expression. The results show the capability of PAW to enhance plant defence mechanisms and, as demonstrated in the field trials, confirmed its ability to improve the health status of the treated plants. Quantitative (q)RT-PCR analyses allowed to determine the transcription level of genes involved in the plant defence response (phenylalanine ammonia-lyase, pal) and in the plant phytoalexin metabolism of PAW-treated materials. The number of symptomatic grapevine plants in vineyards was significantly reduced by the treatments. Transcriptional and post-transcriptional molecular analyses highlighted the PAW ability to enhance the expression of genes encoding the main enzymes involved in the phytoalexin biosynthetic pathway (flavonoids and stilbenes). The PAW ability to enhance some of the plant defence mechanisms also improving the health status of the treated plants was therefore experimentally demonstrated. After three years of trials the overall results demonstrated the possible use of PAW to reduce the disease severity, induce plant resistance both in open field and greenhouse, improving plant healthy status and grapevine yield production

Single-step deposition of hexamethyldisiloxane surface gradient coatings with a high amplitude of water contact angles over a polyethylene foil

One interesting category of nano- and micro-engineered surfaces is surface gradients, which allow the controlled optimization of biointerfaces at a small scale in an extended area length. Plasma coatings offer a large diversity of functionalities at the nanoscale, accompanied by high chemical stability and adhesion on a variety of substrates at ambient temperature. Atmospheric-pressure plasma-assisted deposition could be employed for the generation of surface gradients on thermosensitive materials. In this study, a corona plasma jet is used to deposit polydimethylsiloxane/SiO2-like surface gradients on polyethylene foil by varying the O2 concentration in the discharge during the movement of the plasma source. We obtained, in a single-step approach, gradient coatings along a length of ∼10 cm, with a gradual variation of both chemistry and surface energy

Transcriptional profiling of phytoplasma infected plants treated with plasma activated water (PAW).

Background. Phytoplasmas are insect-transmitted plant pathogenic prokaryotes, associated with severe diseases in agronomic important crops. Management of these diseases has mainly focused on insect vector chemical control and on infected plant rouging. There is therefore a strong need for effective and friendly control strategies for phytoplasma-associated diseases and the possibility to use plasma activated water (PAW) as sustainable and effective method to them was therefore evaluated. PAW is produced by treating distilled water with atmospheric pressure plasmas, inducing the production of reactive oxygen and nitrogen species (RONS) and pH reduction. PAW has good potential for bacterial decontamination, degradation of organic compounds and was shown to positively affect plant growth. Methods. Sterile deionized water (SDW) was exposed to a nanosecond pulsed dielectric barrier discharge, operating in ambient air for 10 min treatment with a peak voltage of 19 kV and a pulse repetition frequency of 1 kHz, which induced production of nitrates, nitrites and peroxides, and a pH decrease. Phytoplasma infected and healthy periwinkles micropropagated shoots were exposed to PAW for about 25 minutes and gene expression studies were then performed. The theses used were: shoots treated with PAW, Fosetyl aluminum (as positive control) and SDW (as negative control), with an exposition of about 25 minutes. Nine shoots for each thesis were then collected at 6 different times after treatment and stored at -80\ub0C. Quantitative RT-PCR analyses were carried out to determine the expression level of genes involved in the plant defense response. Parallel experiments were carried out treating grapevine plants in vineyards previously tested for the phytoplasma presence. Treatments were performed for three years injecting into the plant vascular tissues 10-20 ml of PAW or sterile distilled water (as control) on each selected plant for a total of 60 plants (40 with phytoplasmas and 20 without phytoplasmas). Results. Overexpression of selected genes involved in the phytoalexin metabolism was detected in the periwinkles micropropagated shoots treated with PAW in comparison with the shoots treated with Fosetyl-Al and distilled water. In the field trials, in a relevant number of cases, the PAW-treated symptomatic plants showed reduction of symptoms, while the SDW-treated and untreated plants did not show symptom reduction. No phytotoxicity was observed in the PAW treated grapevine and periwinkle plants. Conclusion. The results obtained showed the capability of PAW to enhance plant defence mechanisms and, as demonstrated in the field trials, confirmed its ability to improve the health status of the treated plant

Earthquake-Related Signals in Central Italy Detected by Hydrogeochemical and Satellite Techniques

Central Apennines are one of the highest seismic risk regions in Italy. A number of energetic events ((Formula presented.) > 5) struck the region during the period 2004–2017, killing several hundreds of people (e.g., 294 casualties associated with the August 24th, 2016, (Formula presented.) 6.0 event of Amatrice). These earthquakes impacted piezometric levels, springs discharges, and groundwater chemistry across a large area, even at distances of dozens of kilometers from the epicenters. Here we present a multidisciplinary dataset based on hydrogeochemical and satellite observations associated with the seismic events that occurred in Central Italy during the period 2004–2017, which combines information derived from the application of groundwater monitoring and satellite techniques. Groundwater monitoring techniques allowed for the detection of hydrogeochemical anomalies in spring and well waters (14 water sampling points in total, with 22 variations larger than (Formula presented.)), while satellite techniques were applied to detect time-space variations in ground thermal emissions. We detected two significant, almost synchronous, anomalies in 2009 and 2016–2017 with both techniques, and we tentatively correlated them to crustal deformation processes. Part of the observed signals were detected before mainshocks, and they appear to be related to aseismic slip or to seismic slip eventually induced by minor fluctuations in seismicity. We argue that the combination of two factors, i.e., the shallow depth of local earthquakes and the concurrent deepening of groundwater circulation paths to several km depth, allow for the recording of variations in the stress field by geofluids released at the surface

Plasma activated water as resistance inducer against bacterial leaf spot of tomato

Plant bacterial diseases are routinely managed with scheduled treatments based on heavy metal compounds or on antibiotics; to reduce the negative environmental impact due to the use of such chemical compounds, as pollution or selection of antibiotic resistant pathogens, the integrated control management is required. In the frame of a sustainable agriculture the use of bacterial antagonists, biological agents, plant defence response elicitors or resistant host plant genotypes are the most effective approaches. In this work, cold atmospheric pressure plasma (CAP) was applied to sterile distilled water, inducing the production of a hydrogen peroxide, nitrite and nitrate, and a pH reduction. In particular, an atmospheric pressure dielectric barrier discharge (DBD) has been used to produce plasma activated water (PAW), that was firstly assayed in in vitro experiments and then in planta through application at the root apparatus of tomato plants, against Xanthomonas vesicatoria (Xv), the etiological agent of bacterial leaf spot. Moreover, the transcription abundance of five genes related to the plant defense was investigated in response to PAW treatment. PAW did not show direct antimicrobial activity against Xv in in vitro experiments, but it enhanced the tomato plants defenses. It was effective in reducing the disease severity by giving relative protections of ca. 61, 51 and 38% when applied 1 h, 24 h and 6 days before the experimental inoculation, respectively. In addition, the experiments highlighted the pal gene involvement in response to the PAW treatments and against the pathogen; its transcription levels resulted significantly high from 1 to 48 h until their decrease 192 h after PAW application