The Problem of Multimodality: What Data-Driven Research Can Tell Us About Online Writing Practices

This article investigates the writing mode, multimodal aspects, and folksonomic elements of digital composition gathered from a WordPress-based ePortfolio platform. Focusing on the student perspective, data was gathered through both surveys of first year students and text analysis of digital compositions in order to produce quantitative results that can be replicated and aggregated. This research demonstrates the impact of assignment design and platform affordances on student composition practices. Results show that incoming students do not fit the “digital native” myth, nor are they prepared to engage in digital scholarship at the college level without significant guidance and specific requirements that scaffold digital work

Positive selection of hearing loss candidate genes,based on multiple microarray platforms experiments and data mining

2006/2007Secondo le stime del World Health Organization, le perdite uditive colpiscono circa 278 milioni di persone in tutto il mondo. Approssimativamente 1 bambino ogni 100, nasce con problemi d’udito. Nonostante l’identificazione negli ultimi 10 anni di più di 100 loci genetici associati a fenotipi di perdita uditiva, non tutti i corrispettivi geni causativi sono stati identificati. Normalmente utilizzando un approccio sperimentale di linkage tradizionale non è sempre possibile identificare un intervallo genomico sufficientemente corto da essere analizzato per la ricerca di mutazioni. Il lavoro presentato in questa tesi ha lo scopo di selezionare un set limitato di geni potenzialmente coinvolti nelle perdite uditive non sindromiche, utilizzando la combinazione di un approccio biologico e bioinformatico. Il punto di partenza dell’analisi è stato il gene GJB2. Il gene GJB2 codifica la Connessina 26, proteina coinvolta nella formazione delle gap junction tra le cellule, ma anche implicata in più del 50% dei casi di perdite uditive non sindromiche. Per questa ragione è stato suggerito un ruolo chiave nella biologia dell’orecchio, che va oltre la sua funzione di proteina canale. In questa tesi è stato esaminato il profilo d’espressione genica di cellule HeLa transfettate con la forma naturale e con delle forme mutate della Connessina26. Le analisi dei dati hanno identificato numerosi geni differenzialmente espressi e si è quindi deciso di passare ad un approccio informatico per ridurne il numero. Questa analisi ha permesso di identificare 19 geni in 11 loci privi di geni causativi selezionandoli in base alla loro espressione rispetto librerie di cDNA prodotte da orecchio. Sono stati quindi identificati i geni omologhi in topo per 5 dei 19 geni, con lo scopo di verificare la loro rilevanza con la perdita uditiva. Per tutti questi 5 geni è stata confermata l’espressione nell’organo di corti in topo e con Real-time RT-PCR nelle linee cellulari transfettate impiegate negli esperimenti di microarray. Il progetto proseguirà ora con lo screening di mutazioni nei geni candidati in famiglie di pazienti selezionate.According to WHO estimates hearing impairment affects 278 million people worldwide. Approximately 1/1000 children are born with a significant hearing impairment. To date approximately 100 genetic loci involved in deafness have been described. Despite the fact that such a large number of genetic locations associated with deafness phenotypes are known, not all the genes involved have been identified yet. Using a traditional linkage approach, however, it is not always possible to map a locus to intervals short enough to be amenable for costly mutation analysis. So far no more than 40 deafness genes have been identified and these encode very heterogeneous proteins. The work presented in this thesis aims to identify a limited set of candidate genes with high potential to be involved in Non-Syndromic Hearing Loss using a combination of biological and bioinformatics approaches. The starting point of the analysis was the GJB2 gene. The GJB2 gene encodes for the gap junction protein Connexin26 and is responsible for more than half of the non-syndromic hearing loss cases. For this reason it has been proposed that this protein might play a wider role in the biology of the ear, beyond its mere channel function. I therefore performed whole genome expression profiles of HeLa cells transfected with the wild type form of the GJB2 gene and compared them to that of cells transfected with mutant forms of this gene to shed light on its function. Initially this experiment yielded a bewildering number of differentially expressed genes (4,984). Thus I devised an in silico strategy to narrow down this number, focusing on genes which were positionally linked to specific non-syndromic hereditary hearing loss conditions, as well as found within human ear cDNA libraries, thus potentially causative of the disease. This further analysis yielded 19 genes within 11 loci. In order to assess their relevance to hearing loss, the mouse homologs of these genes were identified for 5 of them and indeed they were all found to be expressed in the mouse organ of corti. These five genes were also validated by Real-time RT-PCR in the human cell line used for the microarray experiments.197

Hepatitis C virus NS5A targets the nucleosome assembly protein NAP1L1 to control the innate cellular response

Hepatitis C virus (HCV) is a single-stranded positive-sense RNA hepatotropic virus. Despite cellular defenses, HCV is able to replicate in hepatocytes and to establish a chronic infection that could lead to severe complications and hepatocellular carcinoma. An important player in subverting the host response to HCV infection is the viral non-structural protein NS5A that, in addition to its role in replication and assembly, targets several pathways involved in the cellular response to viral infection. Several unbiased screens identified the nucleosome-assembly protein 1-like 1 (NAP1L1) as an interaction partner of HCV NS5A. Here we confirm this interaction and map it to the C-terminus of NS5A of both genotype 1 and 2. NS5A sequesters NAP1L1 in the cytoplasm blocking its nuclear translocation. However, only NS5A from genotype 2 HCV, but not from genotype 1, targets NAP1L1 for proteosomal-mediated degradation. NAP1L1 is a nuclear chaperone involved in chromatin remodeling and we demonstrate the NAP1L1-dependent regulation of specific pathways involved in cellular responses to viral infection and cell survival. Among those we show that lack of NAP1L1 leads to a decrease of RELA protein levels and a strong defect of IRF3 TBK1/IKKϵ-mediated phosphorylation leading to inefficient RIG-I and TLR3 responses. Hence, HCV is able to modulate the host cell environment by targeting NAP1L1 through NS5A

Developmental dyslexia and its complex genetic puzzle

Genetics suggest that DD is an additive or interactive effect of multiple genetic and environmental risk factors. In 2014 an interdisciplinary collaboration between the University of Trieste and the Institute for Maternal and Child Health IRCCS \u201cBurlo Garofolo\u201d of Trieste started, with the aim of performing a genetic study in Italian families with dyslexia

Serum from humans on long ‐ term calorie restriction enhances stress resistance in cell culture

Calorie restriction (CR) without malnutrition is the most robust intervention to slow aging and extend healthy lifespan in experimental model organisms. Several metabolic and molecular adaptations have been hypothesized to play a role in mediating the anti-aging effects of CR, including enhanced stress resistance, reduced oxidative stress and several neuroendocrine modifications. However, little is known about the independent effect of circulating factors in modulating key molecular pathways. In this study, we used sera collected from individuals practicing long-term CR and from age- and sex-matched individuals on a typical US diet to culture human primary fibroblasts and assess the effects on gene expression and stress resistance. We show that treatment of cultured cells with CR sera caused increased expression of stress-response genes and enhanced tolerance to oxidants. Cells cultured in serum from CR individuals showed a 30% increase in resistance to H(2)O(2) damage. Consistently, SOD2 and GPX1 mRNA, two key endogenous antioxidant enzymes, were increased by 2 and 2.5 folds respectively in cells cultured with CR sera. These cellular and molecular adaptations mirror some of the key effects of CR in animals, and further suggest that circulating factors contribute to the CR-mediated protection against oxidative stress and stress-response in humans as well

Role of cyclooxygenae-2 and 5-lypoxygenase polymorphisms in Alzheimer's disease in a population from northern Italy:implications for pharmacogenomics

Alzheimer's disease (AD) is a neurodegenerative disorder clinically characterized by cognitive deficit with progressive worsening of memory. Recent data indicate that neurons, as well as other brain cells, can express enzymes such as cyclooxygenases (COXs) and 5-lipoxygenase (5-LO) which are considered important in inflammatory cells. Moreover, it has been demonstrated that COX-2 and 5-LO enzymes play a considerable role in the pathophysiology of AD. In order to assess the possible role of COX-2 and 5-LO single nucleotide polymorphisms (SNPs) in AD, we examined their distribution in 341 AD patients and 190 controls from Northern Italy. A significant difference was observed in the distribution of the -765G COX-2 and -1708A 5-LO alleles between AD cases and controls (p=0.03 for -765G/C COX-2 SNP; and p=0.007 for -1708G/A 5-LO SNP). Hence, COX-2 -765G and 5-LO -1708A alleles were overrepresented in AD patients and underrepresented in controls. Our data suggest that these alleles of COX-2 and 5-LO could be risk factors for AD. These results seem of some importance for a pharmacogenomic approach

SHIP2: A ‘‘NEW’’ Insulin Pathway Target for Aging Research

Strong evidence suggests that systemic inflammation and central adiposity contribute to and perpetuate metabolic syndrome. All of these alterations predispose individuals to type 2 diabetes mellitus (T2DM), cardiovascular disease, as well as Alzheimer’s disease (AD), all characterized by chronic inflammatory status. On the other hand, extensive abnormalities in insulin and insulin-like growth factor I (IGF-I) and IGF-II signaling mechanisms in brains with AD have been demonstrated, suggesting that AD could be a third form of diabetes. The Src homology domain-containing inositol 5-phosphatase 2 (SHIP2) has an important role in the insulin pathway because its over-expression causes impairment of insulin/IGF-1 signaling. Because some singlenucleotide polymorphisms (SNP) of the gene encoding SHIP2 were significantly associated in T2DM patients with metabolic syndrome and some related conditions, we decided to conduct a case–control study on this gene, analyzing AD and T2DM subjects as cases and young, old, and centenarians as controls. Our results suggest a putative correlation between the the rs144989913 SNP and aging, both successful and unsuccessful, rather than age-related diseases. Because this SNP is an insertion/deletion of 28 bp, it might cause an alteration in SHIP2 expression. It is noteworthy that SHIP2 has been demonstrated to be a potent negative regulator of insulin signaling and insulin sensitivity. Many studies demonstrated the association of the insulin/IGF1 pathway with aging and longevity, so it is tempting to speculate that the found association with SHIP2 and aging might depend on its effect on the insulin/IGF-1 pathwa

Virtual Bodies, Virtual Worlds (ENGL 093A) Final Project

For your final project you will use all of the readings and discussions we have had throughout this semester to inspire your own creation: a virtual reality (VR) or augmented reality (AR) experience intended to teach one of the fictional texts we’ve read. The goal is to educate your audience, particularly to explain or enhance the reading experience through immersive content. You should draw on your own personal experience, criticism of the novel, and other reliable, scholarly sources to write a pitch – and ultimately a formal proposal – for this short extended reality (XR) application. Again, your immersive experience must be both educational and engaging. You will design this simulation as an entry to the competition being held by the NEH

A Public Statement On Our Surveillance Culture: Virtual Bodies, Virtual Worlds (ENGL 093A) Midterm

For your midterm assignment you will design a critical/creative art piece that makes a public statement about our surveillance culture inspired by the materials we have engaged with in this course, including the fictional stories, theoretical texts, and the items from special collections. The piece you make must be created using the resources available through the Makerspace, for example, the laser cutters, sewing material, 3D printers, or crafting materials. Aside from the workshop we will have together, you are encouraged to revisit the Makerspace and book time with the experts available to support your design. Please be respectful of their time and contact them early in the process

Analysis of polymorphisms Leiden Factor V G1691A and prothrombin G20210A as risk factors for acute myocardial infarction.

Thrombotic risk increases in elderly, therefore, the understanding of the genetic predisposition of hypercoagulability could make the difference in the prevention of venous and/or arterial thrombotic events. Laboratory evaluation of hyperfibrinogenemia, increased Factor VII levels, antiphospholipid antibodies presence and hyperhomocysteinemia are considered to have a consistent high predictivity for arterial thrombophilic diseases. Anyway, a large debate exists on the validity of testing Leiden Factor V (FV) G1691A and/or prothrombin (FII) G20210A polymorphisms in patients affected by arterial thrombotic diseases, despite of the several observations described. Here we report data strongly suggesting that at least the FII G20210A polymorphism might be considered an important risk factor for acute myocardial infarction in aged patients (55-80 years old). On the other hand, in spite of a not different genotypic and allelic distribution for the Leiden FV G1691A mutation, the presence of one or both the two polymorphisms is significantly higher among cases than in controls. In conclusion, our data suggest that FII G20210A and/or Leiden FV might be involved as risk factor for arterial disorders in about 5% of old subjects, justifying the opportunity of a genetic screening and an eventual preventive treatment, in particular in old subjects in which other and major risk factors, as hypertension and atherosclerosis, are detected