Book Reviews and Presentations

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SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets

The rapid development of high throughput biotechnologies has led to an onslaught of data describing genetic perturbations and changes in mRNA and protein levels in the cell. Because each assay provides a one-dimensional snapshot of active signaling pathways, it has become desirable to perform multiple assays (e.g. mRNA expression and phospho-proteomics) to measure a single condition. However, as experiments expand to accommodate various cellular conditions, proper analysis and interpretation of these data have become more challenging. Here we introduce a novel approach called SAMNet, for Simultaneous Analysis of Multiple Networks, that is able to interpret diverse assays over multiple perturbations. The algorithm uses a constrained optimization approach to integrate mRNA expression data with upstream genes, selecting edges in the protein–protein interaction network that best explain the changes across all perturbations. The result is a putative set of protein interactions that succinctly summarizes the results from all experiments, highlighting the network elements unique to each perturbation. We evaluated SAMNet in both yeast and human datasets. The yeast dataset measured the cellular response to seven different transition metals, and the human dataset measured cellular changes in four different lung cancer models of Epithelial-Mesenchymal Transition (EMT), a crucial process in tumor metastasis. SAMNet was able to identify canonical yeast metal-processing genes unique to each commodity in the yeast dataset, as well as human genes such as β-catenin and TCF7L2/TCF4 that are required for EMT signaling but escaped detection in the mRNA and phospho-proteomic data. Moreover, SAMNet also highlighted drugs likely to modulate EMT, identifying a series of less canonical genes known to be affected by the BCR-ABL inhibitor imatinib (Gleevec), suggesting a possible influence of this drug on EMT.National Institutes of Health (U.S.) (Grant U54CA112967)National Institutes of Health (U.S.) (Grant R01GN089903)National Science Foundation (U.S.) (Award DB1-0821391)Massachusetts Institute of Technology. Undergraduate Research Opportunities Progra

Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements.

Pooled CRISPR-Cas9 screens are a powerful method for functionally characterizing regulatory elements in the non-coding genome, but off-target effects in these experiments have not been systematically evaluated. Here, we investigate Cas9, dCas9, and CRISPRi/a off-target activity in screens for essential regulatory elements. The sgRNAs with the largest effects in genome-scale screens for essential CTCF loop anchors in K562 cells were not single guide RNAs (sgRNAs) that disrupted gene expression near the on-target CTCF anchor. Rather, these sgRNAs had high off-target activity that, while only weakly correlated with absolute off-target site number, could be predicted by the recently developed GuideScan specificity score. Screens conducted in parallel with CRISPRi/a, which do not induce double-stranded DNA breaks, revealed that a distinct set of off-targets also cause strong confounding fitness effects with these epigenome-editing tools. Promisingly, filtering of CRISPRi libraries using GuideScan specificity scores removed these confounded sgRNAs and enabled identification of essential regulatory elements

Heme Oxygenase-1 Mediates Oxidative Stress and Apoptosis in Coxsackievirus B3-Induced Myocarditis

Background: Heme oxygenase-1 (HO-1), which is suggested to play a role in defending the organism against oxidative stress-mediated injuries, can be induced by diverse factors including viruses and iron. As coxsackievirus B3 (CVB3)-infected SWR/J mice susceptible for chronic myocarditis were found to have a significant iron incorporation and HO-1 upregulation in the myocardium, we aimed to investigate the molecular interplay between HO-1 expression and iron homeostasis in the outcome of viral myocarditis. Methods and Results: In susceptible SWR/J mice, but not in resistant C57BL/6 mice, we observed at later stages of CVB3 myocarditis significant iron deposits in macrophages and also in cardiomyocytes, which were spatially associated with oxidative stress, upregulation of HO-1 and caspase-3 activation. HO-1, which is also expressed in cultivated RAW 264.7 macrophages upon incubation with iron and/or CVB3, could be downregulated by inhibition of NO/iNOS using L-NAME. Moreover, specific inhibition of HO-1 by tin mesoporphyrin revealed a suppression of superoxide production in iron and/or CVB3-treated macrophages. The molecular relationship of HO-1 and caspase-3 activation was proven by downregulation with HO-1 siRNA in iron- and/or CVB3-treated cultivated cells. Importantly, iron was found to increase viral replication in vitro. Conclusion: These results indicate that HO-1 induces a paracrine signalling in macrophages via reactive oxygen species production, mediating apoptosis of heart muscle cells at later stages of myocarditis. Notably, in genetically susceptible mice iron potentiates the detrimental effects of CVB3 by the NO/HO-1 pathway, thus increasing cardiac pathogenicity

Extracting Information for Automatic Indexing of Multimedia Material

This paper discusses our work on information extraction (IE) from multi-lingual, multi-media, multi-genre Language Resources, in a domain where there are many different event types. This work is being carried out in the context of MUMIS, an EU-funded project that aims at the development of basic technology for the creation of a composite index from multiple and multi-lingual sources. Our approach to IE relies on a nite state machinery provided by GATE, a General Architecture for Text Engineering, pipelined with full syntactic analysis and discourse interpretation implemented in Prolog

The Involvement of Photobiology in Contemporary Dentistry—A Narrative Review

Light is an emerging treatment approach that is being used to treat many diseases and conditions such as pain, inflammation, and wound healing. The light used in dental therapy generally lies in visible and invisible spectral regions. Despite many positive results in the treatment of different conditions, this therapy still faces some skepticism, which has prevented its widespread adoption in clinics. The main reason for this skepticism is the lack of comprehensive information about the molecular, cellular, and tissular mechanisms of action, which underpin the positive effects of phototherapy. However, there is currently promising evidence in support of the use of light therapy across a spectrum of oral hard and soft tissues, as well as in a variety of important dental subspecialties, such as endodontics, periodontics, orthodontics, and maxillofacial surgery. The merging of diagnostic and therapeutic light procedures is also seen as a promising area for future expansion. In the next decade, several light technologies are foreseen as becoming integral parts of modern dentistry practice