Segment Routing: a Comprehensive Survey of Research Activities, Standardization Efforts and Implementation Results

Fixed and mobile telecom operators, enterprise network operators and cloud providers strive to face the challenging demands coming from the evolution of IP networks (e.g. huge bandwidth requirements, integration of billions of devices and millions of services in the cloud). Proposed in the early 2010s, Segment Routing (SR) architecture helps face these challenging demands, and it is currently being adopted and deployed. SR architecture is based on the concept of source routing and has interesting scalability properties, as it dramatically reduces the amount of state information to be configured in the core nodes to support complex services. SR architecture was first implemented with the MPLS dataplane and then, quite recently, with the IPv6 dataplane (SRv6). IPv6 SR architecture (SRv6) has been extended from the simple steering of packets across nodes to a general network programming approach, making it very suitable for use cases such as Service Function Chaining and Network Function Virtualization. In this paper we present a tutorial and a comprehensive survey on SR technology, analyzing standardization efforts, patents, research activities and implementation results. We start with an introduction on the motivations for Segment Routing and an overview of its evolution and standardization. Then, we provide a tutorial on Segment Routing technology, with a focus on the novel SRv6 solution. We discuss the standardization efforts and the patents providing details on the most important documents and mentioning other ongoing activities. We then thoroughly analyze research activities according to a taxonomy. We have identified 8 main categories during our analysis of the current state of play: Monitoring, Traffic Engineering, Failure Recovery, Centrally Controlled Architectures, Path Encoding, Network Programming, Performance Evaluation and Miscellaneous...Comment: SUBMITTED TO IEEE COMMUNICATIONS SURVEYS & TUTORIAL

Image Deconvolution Techniques for Single Molecule Studies

One of the principal challenges in the field of biophysics, particularly that of protein-nucleic acid interactions, is the need to analyze information from single proteins as opposed to ensembles of many molecules. Consequently, the advent of high-resolution imaging in single molecule microscopy has enabled researchers to probe the underlying processes of gene regulatory networks and other biological systems. There is, nonetheless, a tradeoff between spatial and temporal resolution, or the ability to localize a molecule in space at increasingly shorter time scales. As such, this dissertation addresses these challenges that hinder single molecule studies by:: i) developing deconvolution techniques in order to localize both immobile and dynamic molecules from their single images with improved spatial and temporal resolution,: ii) determining a protein\u27s diffusive properties with high temporal resolution, and: iii) applying our analytical methods to study model biological systems

Biological correlates of elevated soluble TREM2 in cerebrospinal fluid

Cerebrospinal fluid (CSF) soluble triggering receptor expressed on myeloid cells-2 (sTREM2) is an emerging biomarker of neuroinflammation in Alzheimer's disease (AD). Yet, sTREM2 expression has not been systematically evaluated in relation to concomitant drivers of neuroinflammation. While associations between sTREM2 and tau in CSF are established, we sought to determine additional biological correlates of CSF sTREM2 during the prodromal stages of AD by evaluating CSF Aβ species (Aβx-40), a fluid biomarker of blood-brain barrier integrity (CSF/plasma albumin ratio), and CSF biomarkers of neurodegeneration measured in 155 participants from the Vanderbilt Memory and Aging Project. A novel association between high CSF levels of both sTREM2 and Aβx-40 was observed and replicated in an independent dataset. Aβx-40 levels, as well as the CSF/plasma albumin ratio, explained additional and unique variance in sTREM2 levels above and beyond that of CSF biomarkers of neurodegeneration. The component of sTREM2 levels correlated with Aβx-40 levels best predicted future cognitive performance. We highlight potential contributions of Aβ homeostasis and blood-brain barrier integrity to elevated CSF sTREM2, underscoring novel biomarker associations relevant to disease progression and clinical outcome measures

Chromatin and Epigenetics

Genomics has gathered broad public attention since Lamarck put forward his top-down hypothesis of 'motivated change' in 1809 in his famous book "Philosophie Zoologique" and even more so since Darwin published his famous bottom-up theory of natural selection in "The Origin of Species" in 1859. The public awareness culminated in the much anticipated race to decipher the sequence of the human genome in 2002. Over all those years, it has become apparent that genomic DNA is compacted into chromatin with a dedicated 3D higher-order organization and dynamics, and that on each structural level epigenetic modifications exist. The book "Chromatin and Epigenetics" addresses current issues in the fields of epigenetics and chromatin ranging from more theoretical overviews in the first four chapters to much more detailed methodologies and insights into diagnostics and treatments in the following chapters. The chapters illustrate in their depth and breadth that genetic information is stored on all structural and dynamical levels within the nucleus with corresponding modifications of functional relevance. Thus, only an integrative systems approach allows to understand, treat, and manipulate the holistic interplay of genotype and phenotype creating functional genomes. The book chapters therefore contribute to this general perspective, not only opening opportunities for a true universal view on genetic information but also being key for a general understanding of genomes, their function, as well as life and evolution in general

Fluorescently Labeled siRNAs and their Theranostic Applications in Cancer Gene Therapy

Gene therapy has emerged as a promising precision nano-medicine strategy in the treatment of numerous diseases including cancer. At the forefront of its utility are the applications of short-interfering RNA (siRNA), that silence oncogenic mRNA expression leading to cancer cell death through the RNA interference (RNAi) pathway. Despite the therapeutic potential, siRNAs are limited by poor pharmacological properties, which has hindered their translation into the clinic. Recent studies, however, have highlighted the applications of modified siRNAs, including the use of fluorescent probes and siRNA nanostructures in cancer detection and treatment. The siRNAs reported in this thesis are designed to target and silence the overexpression of the Glucose Regulated Proteins (GRPs) in cancer. The GRPs are a class of chaperone proteins involved in protein folding events within the endoplasmic reticulum. Under physiological or pathological stress, some GRPs translocate to the cell surface where they function as signaling receptors for oncogenic activity. Therefore, cancer cell surface GRPs have been classified as clinically proven biomarkers. Chapter 2 outlines the design, synthesis and characterization of linear as well as novel V- and Y-shape RNA templates with the use of a ribouridine branchpoint synthon. The RNA templates self-assembled into spheres, triangles, squares, pentagons and hexagons of discrete sizes and shapes, confirmed by native PAGE while TEM imaging validated the sizes and shapes of the siRNA nanostructures. Moreover, thermal denaturation and CD spectroscopy were used to ascertain the prerequisite siRNA hybrids for their RNAi applications. Of interest from this initial study, the self-assembled siRNA hybrids (5 nM) that targeted GRP-75, 78 and 95 elicited a synergistic effect, which resulted in potent gene knockdown as well as cancer cell death. The simultaneous integration of therapy and diagnostics (“theranostics”) has been utilized to diagnose and treat cancers at their earliest stages, when they are most likely curable or at least treatable. Building on the work described in Chapter 2, the covalently attachment of fluorescein isothiocyanate (FITC) allowed for monitoring cell uptake and biological activity of a wide range of siRNA motifs. Incorporation of FITC had negligible influence on the A-type helix of the siRNAs, while maintaining good hybrid thermal stability. The FL-siRNAs showed some degree of fluorescence quenching relative to the unlabeled siRNAs. However, the higher-order V- and Y-shape siRNA structures enabled the incorporation of multiple fluorescent reporters, which increased siRNA fluorescence but failed to overcome the quenching effects. Upon transfection within the PC-3 prostate cancer cells, the FL-siRNA hybrids (50 nM) exhibited less mRNA knockdown (~10-30%) when compared to their non-labeled counterparts (~40-80%). Conjugation of the FITC probe to the sense strand of the siRNAs re-established mRNA knockdown (~50

Orthologous proteins of experimental de- and remyelination are differentially regulated in the CSF proteome of multiple sclerosis subtypes

OBJECTIVE: Here, we applied a multi-omics approach (i) to examine molecular pathways related to de- and remyelination in multiple sclerosis (MS) lesions; and (ii) to translate these findings to the CSF proteome in order to identify molecules that are differentially expressed among MS subtypes. METHODS: To relate differentially expressed genes in MS lesions to de- and remyelination, we compared transcriptome of MS lesions to transcriptome of cuprizone (CPZ)-induced de- and remyelination. Protein products of the overlapping orthologous genes were measured within the CSF by quantitative proteomics, parallel reaction monitoring (PRM). Differentially regulated proteins were correlated with molecular markers of inflammation by using MesoScale multiplex immunoassay. Expression kinetics of differentially regulated orthologous genes and proteins were examined in the CPZ model. RESULTS: In the demyelinated and remyelinated corpus callosum, we detected 1239 differentially expressed genes; 91 orthologues were also differentially expressed in MS lesions. Pathway analysis of these orthologues suggested that the TYROBP (DAP12)-TREM2 pathway, TNF-receptor 1, CYBA and the proteasome subunit PSMB9 were related to de- and remyelination. We designed 129 peptides representing 51 orthologous proteins, measured them by PRM in 97 individual CSF, and compared their levels between relapsing (n = 40) and progressive MS (n = 57). Four proteins were differentially regulated among relapsing and progressive MS: tyrosine protein kinase receptor UFO (UFO), TIMP-1, apolipoprotein C-II (APOC2), and beta-2-microglobulin (B2M). The orthologous genes/proteins in the mouse brain peaked during acute remyelination. UFO, TIMP-1 and B2M levels correlated inversely with inflammation in the CSF (IL-6, MCP-1/CCL2, TARC/CCL17). APOC2 showed positive correlation with IL-2, IL-16 and eotaxin-3/CCL26. CONCLUSIONS: Pathology-based multi-omics identified four CSF markers that were differentially expressed in MS subtypes. Upregulated TIMP-1, UFO and B2M orthologues in relapsing MS were associated with reduced inflammation and reflected reparatory processes, in contrast to the upregulated orthologue APOC2 in progressive MS that reflected changes in lipid metabolism associated with increased inflammation