A quantitative assay to monitor HSV-1 ICP0 ubiquitin ligase activity in vitro

The ubiquitin–proteasome system is an essential cellular process that plays a fundamental role in the regulation of protein stability. This pathway is tightly controlled by a sequential cascade of enzymatic steps that culminates in the formation of a poly-ubiquitin chain onto the substrate protein targeted for 26S proteasome degradation. Through a process of co-evolution viruses have evolved mechanisms to utilize or suppress this pathway in order to enhance their replication and spread. One of the first proteins to be expressed during herpes simplex virus 1 (HSV-1) infection is ICP0, a viral RING-finger E3 ubiquitin ligase that targets a variety of cellular proteins for ubiquitination and proteasome-dependent degradation. This activity is required in order for ICP0 to efficiently stimulate the onset of HSV-1 lytic infection and viral reactivation from latency. While it is clear that the RING-finger domain of ICP0 plays an important role in the biology of HSV-1, methods for accurately quantifying its biochemical activity are currently lacking. Here we describe a protocol that enables the quantitative measurement of the ubiquitin ligase activity of ICP0 using near-infrared (IR) western blot imaging. The use of such imaging technology provides an accurate means to examine the biochemical and kinetic parameters of RING-finger ubiquitin ligases in solution, and may provide significant application for inhibitor studies

HSV-1 ICP0: paving the way for viral replication

Herpes simplex virus type 1 (HSV-1) has two distinct phases of its viral life cycle: lytic and latent. One viral immediate-early protein that is responsible for determining the balance between productive lytic replication and reactivation from latency is infected cell protein 0 (ICP0). ICP0 is a 775-amino acid really interesting new gene (RING)-finger-containing protein that possesses E3 ubiquitin ligase activity, which is required for ICP0 to activate HSV-1 gene expression, disrupt nuclear domain (ND) 10 structures, mediate the degradation of cellular proteins, and evade the host cell’s intrinsic and innate antiviral defenses. This article examines our current understanding of ICP0’s transactivating, E3 ubiquitin ligase, and antihost defense activities and their inter-relationships to one another. Lastly, we will discuss how these properties of ICP0 may be utilized as possible targets for HSV-1 antiviral therapies

Source identification for mobile devices, based on wavelet transforms combined with sensor imperfections

One of the most relevant applications of digital image forensics is to accurately identify the device used for taking a given set of images, a problem called source identification. This paper studies recent developments in the field and proposes the mixture of two techniques (Sensor Imperfections and Wavelet Transforms) to get better source identification of images generated with mobile devices. Our results show that Sensor Imperfections and Wavelet Transforms can jointly serve as good forensic features to help trace the source camera of images produced by mobile phones. Furthermore, the model proposed here can also determine with high precision both the brand and model of the device

Semantic scene classification for image annotation and retrieval

We describe an annotation and retrieval framework that uses a semantic image representation by contextual modeling of images using occurrence probabilities of concepts and objects. First, images are segmented into regions using clustering of color features and line structures. Next, each image is modeled using the histogram of the types of its regions, and Bayesian classifiers are used to obtain the occurrence probabilities of concepts and objects using these histograms. Given the observation that a single class with the highest probability is not sufficient to model image content in an unconstrained data set with a large number of semantically overlapping classes, we use the concept/object probabilities as a new representation, and perform retrieval in the semantic space for further improvement of the categorization accuracy. Experiments on the TRECVID and Corel data sets show good performance. © 2008 Springer Berlin Heidelberg

Learning Interpretable Rules for Multi-label Classification

Multi-label classification (MLC) is a supervised learning problem in which, contrary to standard multiclass classification, an instance can be associated with several class labels simultaneously. In this chapter, we advocate a rule-based approach to multi-label classification. Rule learning algorithms are often employed when one is not only interested in accurate predictions, but also requires an interpretable theory that can be understood, analyzed, and qualitatively evaluated by domain experts. Ideally, by revealing patterns and regularities contained in the data, a rule-based theory yields new insights in the application domain. Recently, several authors have started to investigate how rule-based models can be used for modeling multi-label data. Discussing this task in detail, we highlight some of the problems that make rule learning considerably more challenging for MLC than for conventional classification. While mainly focusing on our own previous work, we also provide a short overview of related work in this area.Comment: Preprint version. To appear in: Explainable and Interpretable Models in Computer Vision and Machine Learning. The Springer Series on Challenges in Machine Learning. Springer (2018). See http://www.ke.tu-darmstadt.de/bibtex/publications/show/3077 for further informatio

A Viral Ubiquitin Ligase Has Substrate Preferential SUMO Targeted Ubiquitin Ligase Activity that Counteracts Intrinsic Antiviral Defence

Intrinsic antiviral resistance represents the first line of intracellular defence against virus infection. During herpes simplex virus type-1 (HSV-1) infection this response can lead to the repression of viral gene expression but is counteracted by the viral ubiquitin ligase ICP0. Here we address the mechanisms by which ICP0 overcomes this antiviral response. We report that ICP0 induces the widespread proteasome-dependent degradation of SUMO-conjugated proteins during infection and has properties related to those of cellular SUMO-targeted ubiquitin ligases (STUbLs). Mutation of putative SUMO interaction motifs within ICP0 not only affects its ability to degrade SUMO conjugates, but also its capacity to stimulate HSV-1 lytic infection and reactivation from quiescence. We demonstrate that in the absence of this viral countermeasure the SUMO conjugation pathway plays an important role in mediating intrinsic antiviral resistance and the repression of HSV-1 infection. Using PML as a model substrate, we found that whilst ICP0 preferentially targets SUMO-modified isoforms of PML for degradation, it also induces the degradation of PML isoform I in a SUMO modification-independent manner. PML was degraded by ICP0 more rapidly than the bulk of SUMO-modified proteins in general, implying that the identity of a SUMO-modified protein, as well as the presence of SUMO modification, is involved in ICP0 targeting. We conclude that ICP0 has dual targeting mechanisms involving both SUMO- and substrate-dependent targeting specificities in order to counteract intrinsic antiviral resistance to HSV-1 infection

Mutation analysis of CBP and PCAF reveals rare inactivating mutations in cancer cell lines but not in primary tumours

In this study we screened the histone acetyltransferases CBP and PCAF for mutations in human epithelial cancer cell lines and primary tumours. We identified two CBP truncations (both in cell lines), seven PCAF missense variants and four CBP intronic microdeletions. These data suggest that neither gene is commonly inactivated in human epithelial cancers

A systematic analysis of host factors reveals a Med23-interferon-λ regulatory axis against herpes simplex virus type 1 replication

Herpes simplex virus type 1 (HSV-1) is a neurotropic virus causing vesicular oral or genital skin lesions, meningitis and other diseases particularly harmful in immunocompromised individuals. To comprehensively investigate the complex interaction between HSV-1 and its host we combined two genome-scale screens for host factors (HFs) involved in virus replication. A yeast two-hybrid screen for protein interactions and a RNA interference (RNAi) screen with a druggable genome small interfering RNA (siRNA) library confirmed existing and identified novel HFs which functionally influence HSV-1 infection. Bioinformatic analyses found the 358 HFs were enriched for several pathways and multi-protein complexes. Of particular interest was the identification of Med23 as a strongly anti-viral component of the largely pro-viral Mediator complex, which links specific transcription factors to RNA polymerase II. The anti-viral effect of Med23 on HSV-1 replication was confirmed in gain-of-function gene overexpression experiments, and this inhibitory effect was specific to HSV-1, as a range of other viruses including Vaccinia virus and Semliki Forest virus were unaffected by Med23 depletion. We found Med23 significantly upregulated expression of the type III interferon family (IFN-λ) at the mRNA and protein level by directly interacting with the transcription factor IRF7. The synergistic effect of Med23 and IRF7 on IFN-λ induction suggests this is the major transcription factor for IFN-λ expression. Genotypic analysis of patients suffering recurrent orofacial HSV-1 outbreaks, previously shown to be deficient in IFN-λ secretion, found a significant correlation with a single nucleotide polymorphism in the IFN-λ3 (IL28b) promoter strongly linked to Hepatitis C disease and treatment outcome. This paper describes a link between Med23 and IFN-λ, provides evidence for the crucial role of IFN-λ in HSV-1 immune control, and highlights the power of integrative genome-scale approaches to identify HFs critical for disease progression and outcome

Enyesado para revertir problemas de sodicidad por riego: efecto de fuente y dosis

PosterEvaluar el efecto de fuentes y dosis de yeso sobre distintas propiedades químicas del suelo, y su impacto en el rendimiento de cebada.EEA BalcarceFil: Chevallier Boutell, J. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina.Fil: Carciochi, Walter. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Carciochi, Walter. Instituto Nacional de Tecnología Agropecuaria (INTA) Estación Experimental Agropecuaria Balcarce; Argentina.Fil: García, G.V. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina.Fil: García, G.V. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Diovisalvi, Nicolás, Laboratorio Fertilab; Argentina.Fil: Iglesias, P. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina.Fil: Wyngaard, Nicolás. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina.Fil: Wyngaard, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Crespo, Cecilia. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina.Fil: Crespo, Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Sainz Rozas, Hernán René. Instituto Nacional de Tecnología Agropecuaria (INTA) Estación Experimental Agropecuaria Balcarce; Argentina.Fil: Sainz Rozas, Hernán René. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Reussi Calvo, Nahuel. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina.Fil: Reussi Calvo, Nahuel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina