The structure of insect DNA methyltransferase 2 (DNMT2) DNA binding domain is responsible for the non-CpG methylation in insect genomes

Alignment of vertebrate and invertebrate DNA methyltransferases; 2 (Dnmt2) evidenced an over-all evolutionary conservation of these proteins. However, alignment revealed a vertebrate-specific stretch of about forty amino acids located between the catalytic motif VIII and the target recognition domain that is constantly absent from insect homologues. The analysis of the three-dimensional structure of DNA methyltransferase indicated that this vertebrate specific Dnmt2 portion is located at the DNA binding domain whose structure is essential for the discrimination of the proper target sequence. Insect Dnmt2 enzymes are, therefore, devoid of a portion of the DNA binding domain suggesting that this structural change may alter the methylation target of insect Dnmt2 Making cytosine methylation not limited to the vertebrate canonical CpG but extended to cytosine residues belonging to other dinucleotides

Analysis of heterochromatic epigenetic markers in the holocentric chromosomes of the aphid Acyrthosiphon pisum

Monomethylated-K9 H3 histones (Me9H3) and heterochromatin protein 1 (HP1) are reported as heterochromatin markers in several eukaryotes possessing monocentric chromosomes. In order to confirm that these epigenetic markers are evolutionary conserved, we sequenced the HP1 cDNA and verified the distribution of Me9H3 histones and HP1 in the holocentric chromosomes of the aphid Acyrthosiphon pisum. Sequencing indicates that A. pisum HP1 cDNA (called ApHP1) is 1623 bp long, including a 170 bp long 5’UTR and a 688 bp long 3’UTR. The ApHP1 protein consists in 254 amino acidic residues, has a predicted molecular mass of 28 kDa and a net negative charge. At the structural level, it shows an N terminal chromo domain and a chromo shadow domain at the C terminus linked by a short hinge region. At the cytogenetic level, ApHP1 is located exclusively in the heterochromatic regions of the chromosomes. The same heterochromatic regions were labelled after immuno-staining with antibodies against Me9H3 histones confirming that Hp1 and Me9H3 co-localize at heterochromatic chromosomal areas. Surprisingly, aphid heterochromatin lacks DNA methylation and methylated cytosine residues were mainly spread at euchromatic regions. Finally, the absence of DNA methylation is observed also in aphid rDNA genes that have been repeatedly described as mosaic of methylated and unmethylated units in vertebrates

DNA methylation of fly genes and transposons

The use of anti-5-methylcytosine antibodies in affinity columns allowed the identification of methylated sequences in the genome of Drosophila melanogaster adults. In view of the presence of transposable elements amongst the identified sequences, it has been suggested that DNA methylation is involved in transposon control in the fly genome. On the contrary, a re-analysis of these data can furnish several intriguing elements that could open new questions about the role that DNA methylation plays in the fly genome. The aim of the present paper is to discuss some features that emerge from the analysis of the identified methylated sequences

Advanced microscopic approaches to the study of eukaryotic chromosomes

Since the first discoveries of Schneider and Flemming, several papers have been published on chromosome structure making the understanding of chromatin organization in chromosomes one of the most attractive topics of the current biosciences. Several new discoveries on chromosome structure arose from advanced microscopy techniques that flanked light and electron microscopy. In the present review, the newest microscopy techniques applied to the study of the chromosome structure are presented and discussed in order to evidence the advantages and disadvantages of each approac

Histone methylation and DNA methylation: a missed pas de deux in invertebrates?

Several Authors have reported that histone methylation interacts with DNA methylation creating a self-propagating epigenetic cycle for long-term transcriptional repression of methylated genome compartments. This phenomenon, observed in plant and vertebrate genomes, does not appear to hold true in invertebrates. In particular, both structural and functional evidences suggest that, in invertebrates, DNA methylation and histone methylation do not interact, thus inhibiting the intimate pas de deux observed in other eukaryotes

From Category Theory to Functional Programming: A Formal Representation of Intent

The possibility of managing network infrastructures through software-based programmable interfaces is becoming a cornerstone in the evolution of communication networks. The Intent-Based Networking (IBN) paradigm is a novel declarative approach towards network management proposed by a few Standards Developing Organizations. This paradigm offers a high-level interface for network management that abstracts the underlying network infrastructure and allows the specification of network directives using natural language. Since the IBN concept is based on a declarative approach to network management and programmability, we argue that the use of declarative programming to achieve IBN could uncover valuable insights for this new network paradigm. This paper proposes a formalization of this declarative paradigm obtained with concepts from category theory. Taking this approach to Intent, an initial implementation of this formalization is presented using Haskell, a well-known functional programming language

Ação e impacto de middleboxes presentes na world wide web / Impact and action of middlebox presence in the world wide web

Este trabalho visou investigar a ação de dispositivos, presentes em redes de computadores de forma geral, chamados middleboxes. Além disso a pesquisa visa trazer à luz, em forma de resultados, o impacto e a frequência de atuação desses dispositivos. A pesquisa se deu de forma ampla e global, avaliando diferentes modos de conexão, bem como testando a interação desses dispositivos com diversas características dos dados que trafegam na rede mundial de computadores.

Identification of a new hobo element in the cabbage moth, Mamestra brassicae (Lepidoptera).

A complete hobo-like element, called Mbhobo, was identified in the cabbage moth, Mamestra brassicae. This element has a high sequence similarity to the HFL1 hobo element of Drosophila melanogaster. Amplification of Mbhobo termini indicated that transposition occurred into a 5’-GTGGGTAC-3’ target sequence that was duplicated upon insertion. This target site conforms to the consensus sequence established for the insertion sites of insect hAT elements. Mbhobo has a single 1935 bp long ORF with significant homology to the D. melanogaster HFL1 hobo transposase. FISH experiments evidenced Mbhobo clusters located in heterochromatic regions of Z and W sex chromosomes and in heterochromatic areas of chromosome pair 10

Automated service provisioning in programmable network infrastructures

Modern networks are undergoing a fast and drastic evolution, with software taking a more predominant role. Virtualization and cloud-like approaches are replacing physical network appliances, reducing the management burden of the operators. Furthermore, networks now expose programmable interfaces for fast and dynamic control over traffic forwarding. This evolution is backed by standard organizations such as ETSI, 3GPP, and IETF. This thesis will describe which are the main trends in this evolution. Then, it will present solutions developed during the three years of Ph.D. to exploit the capabilities these new technologies offer and to study their possible limitations to push further the state-of-the-art. Namely, it will deal with programmable network infrastructure, introducing the concept of Service Function Chaining (SFC) and presenting two possible solutions, one with Openstack and OpenFlow and the other using Segment Routing and IPv6. Then, it will continue with network service provisioning, presenting concepts from Network Function Virtualization (NFV) and Multi-access Edge Computing (MEC). These concepts will be applied to network slicing for mission-critical communications and Industrial IoT (IIoT). Finally, it will deal with network abstraction, with a focus on Intent Based Networking (IBN). To summarize, the thesis will include solutions for data plane programming with evaluation on well-known platforms, performance metrics on virtual resource allocations, novel practical application of network slicing on mission-critical communications, an architectural proposal and its implementation for edge technologies in Industrial IoT scenarios, and a formal definition of intent using a category theory approach

From IoT to Cloud: Applications and Performance of the MQTT Protocol

A study of the MQTT publish/subscribe protocol with different QoS levels is presented with the aim to extend the Internet of Things (IoT) concept across access, edge and transport networks and reach cloud computing facilities. A simple testbed is set up with related software components to measure the end-to-end delivery latency between the publisher and the subscribers and the impact of the network delay caused by network configurations with different service deployments. In particular, the latency is shown to rise up to more than 7 times the average network delay when the QoS 2 level is applied, thus indicating that its adoption must be carefully considered