Comparison of the miRNA profiles in HPV-positive and HPV-negative tonsillar tumors and a model system of human keratinocyte clones

Background Better insights into the molecular changes involved in virus-associated and -independent head and neck cancer may advance our knowledge of HNC carcinogenesis and identify critical disease biomarkers. Here we aimed to characterize the expression profiles in a matched set of well-characterized HPV-dependent and HPV-independent tonsillar tumors and equivalent immortalized keratinocyte clones to define potential and clinically relevant biomarkers of HNC of different etiology. Methods Fresh frozen tonsillar cancer tissues were analyzed together with non-malignant tonsillar tissues and compared with cervical tumors and normal cervical tissues. Furthermore, relative miRNAs abundance levels of primary and immortalized human keratinocyte clones were evaluated. The global quantitation of miRNA gene abundance was performed using a TaqMan Low Density Array system. The confirmation of differentially expressed miRNAs was performed on a set of formalin-fixed paraffin-embedded tumor samples enriched for the tumor cell fraction by macrodissection. Results We defined 46 upregulated and 31 downregulated miRNAs characteristic for the HPV-positive tonsillar tumors and 42 upregulated miRNAs and 42 downregulated miRNAs characteristic for HPV-independent tumors. In comparison with the expression profiles in cervical tumors, we defined miR-141-3p, miR-15b-5p, miR-200a-3p, miR-302c-3p, and miR-9-5p as specific for HPV induced malignancies. MiR-335-5p, miR-579-3p, and miR-126-5p were shared by the expression profiles of HPV-positive tonsillar tumors and of the HPV immortalized keratinocyte clones, whereas miR-328-3p, miR-34c-3p, and miR-885-5p were shared by the miRNA profiles of HPV-negative tonsillar tumors and the HPV-negative keratinocytes. Conclusions We identified the miRNAs characteristic for HPV-induced tumors and tonsillar tumors of different etiology, and the results were compared with those of the model system. Our report presents the basis for further investigations leading to the identification of clinically relevant diagnostic and/or therapeutic biomarkers for tumors of viral and non-viral etiology

Towards Reliable and Quantitative Surface‐Enhanced Raman Scattering (SERS): From Key Parameters to Good Analytical Practice

Experimental results obtained in different laboratories world‐wide by researchers using surface‐enhanced Raman scattering (SERS) can differ significantly. We, an international team of scientists with long‐standing expertise in SERS, address this issue from our perspective by presenting considerations on reliable and quantitative SERS. The central idea of this joint effort is to highlight key parameters and pitfalls that are often encountered in the literature. To that end, we provide here a series of recommendations on: a) the characterization of solid and colloidal SERS substrates by correlative electron and optical microscopy and spectroscopy, b) on the determination of the SERS enhancement factor (EF), including suitable Raman reporter/probe molecules, and finally on c) good analytical practice. We hope that both newcomers and specialists will benefit from these recommendations to increase the inter‐laboratory comparability of experimental SERS results and further establish SERS as an analytical tool.Peer Reviewe

Structural and functional basis of mammalian microRNA biogenesis by Dicer

MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is specifically adapted to miRNA biogenesis is unknown. We show that the adaptation entails a unique structural role of Dicer’s DExD/H helicase domain. Although mice tolerate loss of its putative ATPase function, the complete absence of the domain is lethal because it assures high-fidelity miRNA biogenesis. Structures of murine Dicer⋅miRNA precursor complexes revealed that the DExD/H domain has a helicase-unrelated structural function. It locks Dicer in a closed state, which facilitates miRNA precursor selection. Transition to a cleavage-competent open state is stimulated by Dicer-binding protein TARBP2. Absence of the DExD/H domain or its mutations unlocks the closed state, reduces substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning of miRNA and RNAi pathways

Advanced Transactions in Component-Based Software Architectures

This thesis focuses on transaction processing in component-based software architectures, where every component is deployed into a container and client requests may be performed in the scope of a container-interposed transaction. Since every client request is interposed by the container’s delegator objects, a delegator object is able to modify the transaction context in which the requested component method will be executed according to the transaction propagation policy specified along with the component business interface. To address issues determined by the character of component-based software architectures, a novel transaction model called Bourgogne Transactions is introduced. Together with basic significant events (i.e., begin, commit, and abort), Bourgogne Transactions support advanced significant events corresponding to advanced transaction primitives, which allow 1) establishing of flow control dependencies among transactions, 2) one transaction to give permissions to another, and 3) to delegate components from one transaction to another. Opposed to current component-based software architectures, which specify the transaction propagation policy as late as in the deployment descriptor, we propose to specify the transaction propagation policy a

Advanced Transactions in Enterprise JavaBeans

. Enterprise JavaBeans (EJB) is a new technology that aims at supporting distributed transactional component-based applications written in Java. In recent years, a lot of new advanced software applications have arisen, which have new requirements for transaction processing. Since EJB is modern concept that deals with transactions, the paper discusses the support of EJB for those requirements for advanced transactions and identifies weaknesses of transactions in EJB. The paper also proposes an extension of the current transactional concepts in EJB, which can be a remedy for some of the weaknesses identified. The extension, called Bourgogne transactions, allows a transaction to delegate bean objects to other transactions, to share bean objects with other transactions, and to establish flow control dependencies between transactions. Implementation issues together with pitfalls of the proposed extension are discussed. 1

Flexible Framework for Adding Transactions to Components

Abstract: In this paper, we present a flexible framework for extending a component model with transactions. We first discuss key issues of combining components with transactions, and different approaches to achieve an appropriate level of transactional functionality in components. We distinguish between the explicit and implicit component participation approaches that differ by whether a component implements a part of transactional functionality or not. We discuss the influence of both approaches to concurrency control, recovery, and transaction context propagation. Then, we introduce our approach based on the interception pattern. We use several component controllers that manage transactional functionality on behalf of components. We identify several parts of transactional functionality that are implemented by different transactional controllers. For a component, to be transactional, the only requirement is to fulfill a component contract which is specific to various transactional controller implementations. We provide an overview of a prototype implementation of our approach in the Fractal component model. Thanks to the flexibility and reflective nature of Fractal, it is possible to achieve different levels of component transactional functionality by combining different transactional controllers, with only taking their component contracts into account. Our work proves that with an appropriate component framework that supports reflection and flexible component management with clearly defined notions of component composition, lifecycle, and binding, we can add transactions to components in an elegant and flexible way