An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in peach reproductive tissues

Background: Perennial fruit trees display a growth behaviour characterized by annual cycling between growth and dormancy, with complex physiological features. Rosaceae fruit trees represent excellent models for studying not only the fruit growth/patterning but also the progression of the reproductive cycle depending upon the impact of climate conditions. Additionally, current developments in high‐throughput technologies have impacted Rosaceae tree research while investigating genome structure and function as well as (epi)genetic mechanisms involved in important developmental and environmental response processes during fruit tree growth. Among epigenetic mechanisms, chromatin remodelling mediated by histone modifications and other chromatin-related processes play a crucial role in gene modulation, controlling gene expression. Chromatin immunoprecipitation is an effective technique to investigate chromatin dynamics in plants. This technique is generally applied for studies on chromatin states and enrichment of post-transcriptional modifications (PTMs) in histone proteins. Results: Peach is considered a model organism among climacteric fruits in the Rosaceae family for studies on bud formation, dormancy, and organ differentiation. In our work, we have primarily established specific protocols for chromatin extraction and immunoprecipitation in reproductive tissues of peach (Prunus persica). Subsequently, we focused our investigations on the role of two chromatin marks, namely the trimethylation of histone H3 at lysine in position 4 (H3K4me3) and trimethylation of histone H3 at lysine 27 (H3K27me3) in modulating specific gene expression. Bud dormancy and fruit growth were investigated in a nectarine genotype called Fantasia as our model system. Conclusions: We present general strategies to optimize ChIP protocols for buds and mesocarp tissues of peach and analyze the correlation between gene expression and chromatin mark enrichment/depletion. The procedures proposed may be useful to evaluate any involvement of histone modifications in the regulation of gene expression during bud dormancy progression and core ripening in fruits

Ex ante versus ex post regulation of bank capital

The current debate on the new Basel Accord gives rise to a natural question about the appropriate form of capital regulation. We construct a simple framework to analyze this ssue. In our model the risk carried by a bank as well as managerial risk preference are a bank’s private information. We show that ex ante constraints waste the superior risk information of a bank, while an ex post regime makes full use of it. However, the latter is more vulnerable to the problem of unknown managerial risk-aversion. The results imply that the two regimes are complements, rather than substitutes. Further, under plausible conditions, an ex post regime emerges as the dominant element of the optimal combination. We use the results to shed light on current policy concerns. In particular, our results provides theoretical underpinning for the inclusion of pillar 2 alongside pillar 1 in Basel II

Transcriptional regulation of MdmiR285N microRNA in apple (Malus x domestica) and the heterologous plant system Arabidopsis thaliana

Malus x domestica microRNA MdmiR285N is a potential key regulator of plant immunity, as it has been predicted to target 35 RNA transcripts coding for different disease resistance proteins involved in plant defense to pathogens. In this study, the promoter region of MdmiR285N was isolated from the apple genome and analyzed in silico to detect potential regulatory regions controlling its transcription. A complex network of putative regulatory elements involved in plant growth and development, and in response to different hormones and stress conditions, was identified. Activity of the \u3b2-Glucoronidase (GUS) reporter gene driven by the promoter of MdmiR285N was examined in transgenic apple, demonstrating that MdmiR285N was expressed during the vegetative growth phase. Similarly, in transgenic Arabidopsis thaliana, spatial and temporal patterns of GUS expression revealed that MdmiR285N was differentially regulated during seed germination, vegetative phase change, and reproductive development. To elucidate the role of MdmiR285N in plant immunity, MdmiR285N expression in wild-type apple plants and GUS activity in transgenic apple and Arabidopsis thaliana plants were monitored in response to Erwinia amylovora and Pseudomonas syringae pv. Tomato DC3000. A significant decrease of MdmiR285N levels and GUS expression was observed during host-pathogen infections. Overall, these data suggest that MdmiR285N is involved in the biotic stress response, plant growth, and reproductive development

Leaf monoterpene emission limits photosynthetic downregulation under heat stress in field-grown grapevine

Rising temperature is among the most remarkably stressful phenomena induced by global climate changes with negative impacts on crop productivity and quality. It has been previously shown that volatiles belonging to the isoprenoid family can confer protection against abiotic stresses. In this work, two Vitis vinifera cv. ‘Chardonnay’ clones (SMA130 and INRA809) differing due to a mutation (S272P) of the DXS gene encoding for 1-deoxy-D-xylulose-5-phosphate (the first dedicated enzyme of the 2C-methyl-D-erythritol-4-phosphate (MEP) pathway) and involved in the regulation of isoprenoids biosynthesis were investigated in field trials and laboratory experiments. Leaf monoterpene emission, chlorophyll fluorescence and gas-exchange measurements were assessed over three seasons at different phenological stages and either carried out in in vivo or controlled conditions under contrasting temperatures. A significant (p < 0.001) increase in leaf monoterpene emission was observed in INRA809 when plants were experiencing high temperatures and over two experiments, while no differences were recorded for SMA130. Significant variation was observed for the rate of leaf CO2 assimilation under heat stress, with INRA809 maintaining higher photosynthetic rates and stomatal conductance values than SMA130 (p = 0.003) when leaf temperature increased above 30 °C. At the same time, the maximum photochemical quantum yield of PSII (Fv/Fm) was affected by heat stress in the non-emitting clone (SMA130), while the INRA809 showed a significant resilience of PSII under elevated temperature conditions. Consistent data were recorded between field seasons and temperature treatments in controlled environment conditions, suggesting a strong influence of monoterpene emission on heat tolerance under high temperatures. This work provides further insights on the photoprotective role of isoprenoids in heat-stressed Vitis vinifera, and additional studies should focus on unraveling the mechanisms underlying heat tolerance on the monoterpene-emitter grapevine clone

Dual analysis of host and pathogen transcriptomes in ostreid herpesvirus 1-positive Crassostrea gigas

Ostreid herpesvirus type 1 (OsHV-1) has become a problematic infective agent for the Pacific oyster Crassostrea gigas. In particular, the OsHV-1 \u3bcVar subtype has been associated with severe mortality episodes in oyster spat and juvenile oysters in France and other regions of the world. Factors enhancing the infectivity of the virus and its interactions with susceptible and resistant bivalve hosts are still to be understood, and only few studies have explored the expression of oyster or viral genes during productive infections. In this work, we have performed a dual RNA sequencing analysis on an oyster sample with a high viral load. High sequence coverage allowed us to thoroughly explore the OsHV-1 transcriptome and identify the activated molecular pathways in C.gigas. The identification of several highly induced and defence-related oyster transcripts supports the crucial role played by the innate immune system against the virus and opportunistic microbes possibly contributing to subsequent spat mortality

A two-step, user-centered approach to personalized tourist recommendations

Geo-localized, mobile applications can simplify a tourist visit, making the relevant Point of Interests more easily and promptly discernible to users. At the same time, such solutions must avoid creating unfitting or rigid user profiles that impoverish the users' options instead of refining them. Currently, user profiles in recommender systems rely on dimensions whose relevance to the user is more often presumed than empirically defined. To avoid this drawback, we build our recommendation system in a two-step process, where profile parameters are evaluated preliminarily and separately from the recommendations themselves. We describe this two-step evaluation process including an initial survey (N=206), and a subsequent controlled study (N=24). We conclude by emphasizing the benefit and generalizability of the approach

Effects of combined drug treatments on Plasmodium falciparum : in vitro assays with doxycycline, ivermectin and efflux pump inhibitors

There is great concern regarding the rapid emergence and spread of drug-resistance in Plasmodium falciparum, the parasite responsible for the most severe form of human malaria. Parasite populations resistant to some or all the currently available antimalarial treatments are present in different world regions. Considering the need for novel and integrated approaches to control malaria, combinations of drugs were tested on P. falciparum. The primary focus was on doxycycline, an antibiotic that specifically targets the apicoplast of the parasite. In combination with doxycycline, three different drugs known to inhibit efflux pumps (verapamil, elacridar and ivermectin) were tested, with the assumption that they could increase the intracellular concentration of the antibiotic and consequently its efficacy against P. falciparum. We emphasize that elacridar is a third-generation ABC transporters inhibitor, never tested before on malaria parasites. In vitro experiments were performed on asexual stages of two strains of P. falciparum, chloroquine-sensitive (D10) and chloroquineresistant (W2). Incubation times on asynchronous or synchronous cultures were 72h or 96h, respectively. The antiplasmodial effect (i.e. the IC50) was determined by measuring the activity of the parasite lactate dehydrogenase, while the interaction between drugs was determined through combination index (CI) analyses. Elacridar achieved an IC50 concentration comparable to that of ivermectin, approx. 10-fold lower than that of verapamil, the other tested ABC transporter inhibitor. CI results showed synergistic effect of verapamil plus doxycycline, which is coherent with the starting hypothesis, i.e. that ABC transporters represent potential targets, worth of further investigations, towards the development of companion molecules useful to enhance the efficacy of antimalarial drugs. At the same time, the observed antagonistic effect of doxycycline in combination with ivermectin or elacridar highlighted the importance of drug testing, to avoid the de-facto generation of a sub-dosage, a condition that facilitates the development of drug resistance

A multilevel carbon and water footprint dataset of food commodities

Informing and engaging citizens to adopt sustainable diets is a key strategy for reducing global environmental impacts of the agricultural and food sectors. In this respect, the first requisite to support citizens and actors of the food sector is to provide them a publicly available, reliable and ready to use synthesis of environmental pressures associated to food commodities. Here we introduce the SU-EATABLE LIFE database, a multilevel database of carbon (CF) and water (WF) footprint values of food commodities, based on a standardized methodology to extract information and assign optimal footprint values and uncertainties to food items, starting from peer-reviewed articles and grey literature. The database and its innovative methodological framework for uncertainty treatment and data quality assurance provides a solid basis for evaluating the impact of dietary shifts on global environmental policies, including climate mitigation through greenhouse gas emission reductions. The database ensures repeatability and further expansion, providing a reliable science-based tool for managers and researcher in the food sector

HPPD-Inhibiting herbicides alone or in tank-mix with Atrazine in elephant grass.

The interference imposed by weeds is one of the most important factors limiting elephant grass forage yield. Two experiments were carried out in 2015/2016 and 2017 to evaluate the selectivity and weed control of 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibiting herbicides applied alone or in combination with atrazine in elephant grass. The treatments applied in the experiment conducted in Valença, Rio de Janeiro State, Brazil, were as follows: two rates of mesotrione (0.072 and 0.144 kg ha-1 + 0.5% v/v mineral oil - Assist®), two rates of tembotrione (0.075 and 0.100 kg ha-1 + 0.5% v/v mineral oil - Aureo®), atrazine + mesotrione (1.25 + 0.072 kg ha-1 + 0.5% v/v mineral oil - Assist®), atrazine + tembotrione (1.25 + 0.100 kg ha-1 + 0.5% v/v mineral oil - Aureo®), atrazine + mesotrione (1.25 + 0.072 kg ha-1), atrazine + tembotrione (1.25 + 0.100 kg ha-1) and two checks (weed-free check and weedy check). The same herbicide treatments and a check without application were applied in an experiment conducted in Coronel Pacheco, Minas Gerais State, Brazil. Two application rates of mesotrione with the addition of mineral oil or the tank mixture of atrazine plus mesotrione, with or without the addition of mineral oil, did not provide injuries capable to reduce elephant grass forage yield. Tembotrione was phytotoxic to elephant grass when applied with mineral oil. Atrazine plus tembotrione in a tank-mix, with or without mineral oil, were also phytotoxic to elephant grass. All treatments provided satisfactory weed control