Matthew Smith

NS2/NEP protein regulates transcription and replication of the influenza virus RNA genome.

The influenza virus RNA polymerase transcribes the negative-sense viral RNA segments (vRNA) into mRNA and replicates them via complementary RNA (cRNA) intermediates into more copies of vRNA. It is not clear how the relative amounts of the three RNA products, mRNA, cRNA and vRNA, are regulated during the viral life cycle. We found that in viral ribonucleoprotein (vRNP) reconstitution assays involving only the minimal components required for viral transcription and replication (the RNA polymerase, the nucleoprotein and a vRNA template), the relative levels of accumulation of RNA products differed from those observed in infected cells, suggesting a regulatory role for additional viral proteins. Expression of the viral NS2/NEP protein in RNP reconstitution assays affected viral RNA levels by reducing the accumulation of transcription products and increasing the accumulation of replication products to more closely resemble those found during viral infection. This effect was functionally conserved in influenza A and B viruses and was influenza-virus-type-specific, demonstrating that the NS2/NEP protein changes RNA levels by specific alteration of the viral transcription and replication machinery, rather than through an indirect effect on the host cell. Although NS2/NEP has been shown previously to play a role in the nucleocytoplasmic export of viral RNPs, deletion of the nuclear export sequence region that is required for its transport function did not affect the ability of the protein to regulate RNA levels. A role for the NS2/NEP protein in the regulation of influenza virus transcription and replication that is independent of its viral RNP export function is proposed.

Association of the Influenza A Virus RNA-Dependent RNA Polymerase with Cellular RNA Polymerase II

ABSTRACT Transcription by the influenza virus RNA-dependent RNA polymerase is dependent on cellular RNA processing activities that are known to be associated with cellular RNA polymerase II (Pol II) transcription, namely, capping and splicing. Therefore, it had been hypothesized that transcription by the viral RNA polymerase and Pol II might be functionally linked. Here, we demonstrate for the first time that the influenza virus RNA polymerase complex interacts with the large subunit of Pol II via its C-terminal domain. The viral polymerase binds hyperphosphorylated forms of Pol II, indicating that it targets actively transcribing Pol II. In addition, immunofluorescence analysis is consistent with a new model showing that influenza virus polymerase accumulates at Pol II transcription sites. The present findings provide a framework for further studies to elucidate the mechanistic principles of transcription by a viral RNA polymerase and have implications for the regulation of Pol II activities in infected cells.

The PA Subunit Is Required for Efficient Nuclear Accumulation of the PB1 Subunit of the Influenza A Virus RNA Polymerase Complex

ABSTRACT The RNA genome of influenza virus is transcribed and replicated by the viral RNA polymerase complex in the cell nucleus. We have generated green fluorescent protein (GFP)-tagged polymerase subunits to study the assembly of the polymerase complex. Our results show that individually expressed polymerase basic protein 1 (PB1) and polymerase acidic protein (PA) subunits were distributed in both the cytoplasm and the nucleus, while the polymerase basic protein 2 (PB2) subunit accumulated in the nucleus. Although it has been reported that PB1 alone accumulates in the nucleus, we demonstrate that PB1 requires the coexpression of PA for efficient nuclear accumulation. Our results support a model which proposes that PB1 and PA are transported into the nucleus as a complex.

The effect of scale-free topology on the robustness and evolvability of genetic regulatory networks

We investigate how scale-free (SF) and Erdos-Rényi (ER) topologies affect the interplay between evolvability and robustness of model gene regulatory networks with Boolean threshold dynamics. In agreement with Oikonomou and Cluzel (2006) we find that networks with SF(in) topologies, that is SF topology for incoming nodes and ER topology for outgoing nodes, are significantly more evolvable towards specific oscillatory targets than networks with ER topology for both incoming and outgoing nodes. Similar results are found for networks with SF(both) and SF(out) topologies. The functionality of the SF(out) topology, which most closely resembles the structure of biological gene networks (Babu et al., 2004), is compared to the ER topology in further detail through an extension to multiple target outputs, with either an oscillatory or a non-oscillatory nature. For multiple oscillatory targets of the same length, the differences between SF(out) and ER networks are enhanced, but for non-oscillatory targets both types of networks show fairly similar evolvability. We find that SF networks generate oscillations much more easily than ER networks do, and this may explain why SF networks are more evolvable than ER networks are for oscillatory phenotypes. In spite of their greater evolvability, we find that networks with SF(out) topologies are also more robust to mutations (mutational robustness) than ER networks. Furthermore, the SF(out) topologies are more robust to changes in initial conditions (environmental robustness). For both topologies, we find that once a population of networks has reached the target state, further neutral evolution can lead to an increase in both the mutational robustness and the environmental robustness to changes in initial conditions.

Assessing the impact of aviation security on cyber power

We analyse the impact of new wireless technology threat models on cyber power, using the aviation context as an example. The ongoing move from traditional air traffic control systems such as radar and voice towards enhanced surveillance and communications systems using modern data networks causes a marked shift in the security of the aviation environment. Implemented through the European SESAR and the US American NextGen programmes, several new air traffic control and communication protocols are currently being rolled out that have been in the works for decades. Unfortunately, during their development the shifting wireless technology threat models were not taken into account. As technology related to digital avionics is getting more widely accessible, traditional electronic warfare threat models are fast becoming obsolete. This paper defines a novel and realistic threat model based on the up-to-date capabilities of different types of threat agents and their impact on a digitalised aviation communication system. After analysing how the changing technological environment affects the security of aviation technologies, current and future, we discuss the reasons preventing the aviation industry from quickly improving the security of its wireless protocols. Among these reasons, we identify the existing tradition of the industry, the prevalence of legacy hard- and software, major cost pressures, slow development cycles, and a narrow focus on safety (as opposed to security). Finally, we analyse how this major technological shift informs the future of cyber power and conflict in the aviation environment by looking at tangible effects for state actors.

OpenSky report 2016: Facts and figures on SSR mode S and ADS-B usage

This paper provides up-to-date statistics on SSR Mode S and 1090ES ADS-B usage from the OpenSky Network. By analyzing the large host of real-world data collected by OpenSky, we provide insights on the current composition of Mode S downlink communications, aircraft equipage, interrogation patterns and much more. We publish up-to-date, empirically validated numbers on the status of the ongoing ADS-B deployment based on data collected over large areas in Europe, North America, and New Zealand, and categorize these aircraft by incorporating publicly available data sources.

On the security and privacy of ACARS

Aircraft Communications Addressing and Reporting System . Standardised in 1978 by ARINC . Supports Airline Administrative Control (AAC) and Air Traffic Management (ATM) .

Crowdsourcing security for wireless air traffic communications

Protecting the security of the cyber-physical systems that make up the worlds critical infrastructures has been a recent hotly debated topic. Legacy wireless communication infrastructure is often an impediment to quickly improving these crucial systems, as cryptographic solutions prove impossible to deploy. In this article, we propose the establishment of a separate verification layer for sensitive wireless data powered by crowdsourced sensors connected to the Internet and apply it to the aviation domain. We first validate the need for independent data verification in air traffic control networks, where all wireless communication is conducted in the clear and thus subject to manipulation. To counter this threat, we develop a comprehensive model for the verification of wireless communication based on massively distributed data collection and outline how it can be used to immediately improve the security of unprotected air traffic control networks. By combining several different methods based on the content and the physical characteristics of aircraft signals, our system is able to detect typical injection, modification and jamming attacks. We further develop a trust model to defend against potential insider threats based on compromised sensors. We illustrate our approach using the crowdsourced sensor network OpenSky, which captures large parts of civil air traffic communication around the globe. We analyse the security of our approach and show that it can quickly, cheaply, and effectively defend against even sophisticated attacks.

Economy Class Crypto: Exploring Weak Cipher Usage in Avionic Communications via ACARS

Recent research has shown that a number of existing wireless avionic systems lack encryption and are thus vulnerable to eavesdropping and message injection attacks. The Aircraft Communications Addressing and Reporting System (ACARS) is no exception to this rule with 99% of the traffic being sent in plaintext. However, a small portion of the traffic coming mainly from privately-owned and government aircraft is encrypted, indicating a stronger requirement for security and privacy by those users. In this paper, we take a closer look at this protected communication and analyze the cryptographic solution being used. Our results show that the cipher used for this encryption is a mono-alphabetic substitution cipher, broken with little effort. We assess the impact on privacy and security to its unassuming users by characterizing months of real-world data, decrypted by breaking the cipher and recovering the keys. Our results show that the decrypted data leaks privacy sensitive information including existence, intent and status of aircraft owners.

Undermining Privacy in the Aircraft Communications Addressing and Reporting System (ACARS)

Abstract Despite the Aircraft Communications, Addressing and Reporting System (ACARS) being widely deployed for over twenty years, little scrutiny has been applied to it outside of the aviation community. Whilst originally utilized by commercial airlines to track their flights and provide automated timekeeping on crew, today it serves as a multi-purpose air-ground data link for many aviation stakeholders including private jet owners, state actors and military. Such a change has caused ACARS to be used far beyond its original mandate; to date no work has been undertaken to assess the extent of this especially with regard to privacy and the various stakeholder groups which use it. In this paper, we present an analysis of ACARS usage by privacy sensitive actors-military, government and business. We conduct this using data from the VHF (both traditional ACARS, and VDL mode 2) and satellite communications subnetworks. Based on more than two million ACARS messages collected over the course of 16 months, we demonstrate that current ACARS usage systematically breaches location privacy for all examined aviation stakeholder groups, explaining the types of messages used to cause this problem.We illustrate the challenges with three case studies-one for each stakeholder group-to show how much privacy sensitive information can be constructed with a handful of ACARS messages. We contextualize our findings with opinions on the issue of privacy in ACARS from 40 aviation industry professionals. From this, we explore recommendations for how to address these issues, including use of encryption and policy measures.