Characterization of the lncRNA transcriptome in mESC-derived motor neurons: Implications for FUS-ALS

Long non-coding RNAs (lncRNAs) are currently recognized as crucial players in nervous system development, function and pathology. In Amyotrophic Lateral Sclerosis (ALS), identification of causative mutations in FUS and TDP-43 or hexanucleotide repeat expansion in C9ORF72 point to the essential role of aberrant RNA metabolism in neurodegeneration. In this study, by taking advantage of an in vitro differentiation system generating mouse motor neurons (MNs) from embryonic stem cells, we identified and characterized the long non-coding transcriptome of MNs. Moreover, by using mutant mouse MNs carrying the equivalent of one of the most severe ALS-associated FUS alleles (P517L), we identified lncRNAs affected by this mutation. Comparative analysis with humanMNs derived in vitro frominduced pluripotent stemcells indicated that candidate lncRNAs are conserved between mouse and human. Our work provides a global view of the long non-coding transcriptome of MN, as a prerequisite toward the comprehension of the still poorly characterized non-coding side ofMNphysiopatholog

Regulating Data Exchange in Service Oriented Applications

We define a type system for COWS, a formalism for specifying and combining services, while modelling their dynamic behaviour. Our types permit to express policies constraining data exchanges in terms of sets of service partner names attachable to each single datum. Service programmers explicitly write only the annotations necessary to specify the wanted policies for communicable data, while a type inference system (statically) derives the minimal additional annotations that ensure consistency of services initial configuration. Then, the language dynamic semantics only performs very simple checks to authorize or block communication. We prove that the type system and the operational semantics are sound. As a consequence, we have the following data protection property: services always comply with the policies regulating the exchange of data among interacting services. We illustrate our approach through a simplified but realistic scenario for a service-based electronic marketplace

A Regulatory Circuitry Between Gria2, miR-409, and miR-495 Is Affected by ALS FUS Mutation in ESC-Derived Motor Neurons

Mutations in fused in sarcoma (FUS) cause amyotrophic lateral sclerosis (ALS). FUS is a multifunctional protein involved in the biogenesis and activity of several types of RNAs, and its role in the pathogenesis of ALS may involve both direct effects of disease-associated mutations through gain- and loss-of-function mechanisms and indirect effects due to the cross talk between different classes of FUS-dependent RNAs. To explore how FUS mutations impinge on motor neuron-specific RNA-based circuitries, we performed transcriptome profiling of small and long RNAs of motor neurons (MNs) derived from mouse embryonic stem cells carrying a FUS-P517L knock-in mutation, which is equivalent to human FUS-P525L, associated with a severe and juvenile-onset form of ALS. Combining ontological, predictive and molecular analyses, we found an inverse correlation between several classes of deregulated miRNAs and their corresponding mRNA targets in both homozygous and heterozygous P517L MNs. We validated a circuitry in which the upregulation of miR-409-3p and miR-495-3p, belonging to a brainspecific miRNA subcluster implicated in several neurodevelopmental disorders, produced the downregulation of Gria2, a subunit of the glutamate α‐amino‐3‐hydroxy‐5‐methyl-4-isoxazole propionic acid (AMPA) receptor with a significant role in excitatory neurotransmission. Moreover, we found that FUS was involved in mediating such miRNA repression. Gria2 alteration has been proposed to be implicated in MN degeneration, through disturbance of Ca2+ homeostasis, which triggers a cascade of damaging “excitotoxic” events. The molecular cross talk identified highlights a role for FUS in excitotoxicity and in miRNA-dependent regulation of Gria2. This circuitry also proved to be deregulated in heterozygosity, which matches the human condition perfectly

Stochastic modeling and analysis of the bitcoin protocol in the presence of block communication delays

International audienceWe analyze the protocol of the Bitcoin blockchain by using the PRISM probabilistic model checker. In particular, we (i) extend PRISM with the ledger data type, (ii) model the behaviour of the key participants in the protocol-the miners-and (iii) describe the whole protocol as a parallel composition of processes. The probabilistic analysis of the model highlights how forks happen and how they depend on specific parameters of the protocol, such as the difficulty of the cryptopuzzle and the network communication delays. Our results confirm that considering transactions in blocks at depth larger than 5 as permanent is reasonable because the majority of miners have consistent blockchains up-to that depth with probability of almost 1. We also study the behaviour of networks with churn miners, which may leave the network and rejoin afterwards, and with different topologies

A Calculus for Orchestration of Web Services

We introduce COWS (Calculus for Orchestration of Web Services), a new foundational language for SOC whose design has been influenced by WS-BPEL, the de facto standard language for orchestration of web services. COWS combines in an original way a number of ingredients borrowed from well-known process calculi, e.g. asynchronous communication, polyadic synchronization, pattern matching, protection, delimited receiving and killing activities, while resulting different from any of them. Several examples illustrates COWS peculiarities and show its expressiveness both for modelling imperative and orchestration constructs, e.g. web services, flow graphs, fault and compensation handlers, and for encoding other process and orchestration languages

J Vis Exp

The last decades have witnessed the explosion of scientific interest around gene expression control mechanisms at the RNA level. This branch of molecular biology has been greatly fueled by the discovery of noncoding RNAs as major players in post-transcriptional regulation. Such a revolutionary perspective has been accompanied and triggered by the development of powerful technologies for profiling short RNAs expression, both at the high-throughput level (genome-wide identification) or as single-candidate analysis (steady state accumulation of specific species). Although several state-of-art strategies are currently available for dosing or visualizing such fleeing molecules, Northern Blot assay remains the eligible approach in molecular biology for immediate and accurate evaluation of RNA expression. It represents a first step toward the application of more sophisticated, costly technologies and, in many cases, remains a preferential method to easily gain insights into RNA biology. Here we overview an efficient protocol (Enhanced Northern Blot) for detecting weakly expressed microRNAs (or other small regulatory RNA species) from Drosophila melanogaster whole embryos, manually dissected larval/adult tissues or in vitro cultured cells. A very limited amount of RNA is required and the use of material from flow cytometry-isolated cells can be also envisaged

FUS affects circular RNA expression in murine embryonic stem cell-derived motor neurons

The RNA-binding protein FUS participates in several RNA biosynthetic processes and has been linked to the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. Here we report that FUS controls back-splicing reactions leading to circular RNA (circRNA) production. We identified circRNAs expressed in in vitro -derived mouse motor neurons (MNs) and determined that the production of a considerable number of these circRNAs is regulated by FUS. Using RNAi and overexpression of wild-type and ALS-asso- ciated FUS mutants, we directly correlate the modulation of circRNA biogenesis with alteration of FUS nuclear levels and with putative toxic gain of function activities. We also demonstrate that FUS regulates circRNA biogenesis by binding the introns flanking the back-splicing junctions and that this control can be reproduced with artificial constructs. Most circRNAs are conserved in humans and specific ones are deregulated in human-induced pluripotent stem cell-derived MNs carrying the FUS P525L mutation associated with AL

Enhancing nonclassical bosonic correlations in a quantum walk network through experimental control of disorder

The presence of disorder and inhomogeneities in quantum networks has often been unexpectedly beneficial for both quantum and classical resources. Here we experimentally realize a controllable inhomogenous quantum walk (QW) dynamics, which can be exploited to investigate the effect of coherent disorder on the quantum correlations between two indistinguishable photons. Through the imposition of suitable disorder configurations, we observe two-photon states that exhibit an enhancement in the quantum correlations between two selected modes of the network, compared to the case of an ordered QW. Different configurations of disorder can steer the system toward different realizations of such an enhancement, thus allowing spatial and temporal manipulation of quantum correlations between remote modes of QW networks

Fire Occurrences and Greenhouse Gas Emissions from Deforestation in the Brazilian Amazon.

Abstract: This work presents the dynamics of fire occurrences, greenhouse gas (GHG) emissions, forest clearing, and degradation in the Brazilian Amazon during the period 2006?2019, which includes the approval of the new Brazilian Forest Code in 2012. The study was carried out in the Brazilian Amazon, Pará State, and the municipality of Novo Progresso (Pará State). The analysis was based on deforestation and fire hotspot datasets issued by the Brazilian Institute for Space Research (INPE), which is produced based on optical and thermal sensors onboard different satellites. Deforestation data was also used to assess GHG emissions from the slash-and-burn practices. The work showed a good correlation between the occurrence of fires in the newly deforested area in the municipality of Novo Progresso and the slash-and-burn practices. The same trend was observed in the Pará State, suggesting a common practice along the deforestation arch. The study indicated positive coefficients of determination of 0.72 and 0.66 between deforestation and fire occurrences for the municipality of Novo Progresso and Pará State, respectively. The increased number of fire occurrences in the primary forest suggests possible ecosystem degradation. Deforestation reported for 2019 surpassed 10,000 km2, which is 48% higher than the previous ten years, with an average of 6760 km2. The steady increase of deforestation in the Brazilian Amazon after 2012 has been a worldwide concern because of the forest loss itself as well as the massive GHG emitted in the Brazilian Amazon. We estimated 295 million tons of net CO2, which is equivalent to 16.4% of the combined emissions of CO2 and CH4 emitted by Brazil in 2019. The correlation of deforestation and fire occurrences reported from satellite images confirmed the slash-and-burn practice and the secondary effect of deforestation, i.e., degradation of primary forest surrounding the deforested areas. Hotspots? location was deemed to be an important tool to verify forest degradation. The incidence of hotspots in forest area is from 5% to 20% of newly slashed-and-burned areas, which confirms the strong impact of deforestation on ecosystem degradation due to fire occurrences over the Brazilian Amazon