Trustworthy Knowledge Planes For Federated Distributed Systems

In federated distributed systems, such as the Internet and the public cloud, the constituent systems can differ in their configuration and provisioning, resulting in significant impacts on the performance, robustness, and security of applications. Yet these systems lack support for distinguishing such characteristics, resulting in uninformed service selection and poor inter-operator coordination. This thesis presents the design and implementation of a trustworthy knowledge plane that can determine such characteristics about autonomous networks on the Internet. A knowledge plane collects the state of network devices and participants. Using this state, applications infer whether a network possesses some characteristic of interest. The knowledge plane uses attestation to attribute state descriptions to the principals that generated them, thereby making the results of inference more trustworthy. Trustworthy knowledge planes enable applications to establish stronger assumptions about their network operating environment, resulting in improved robustness and reduced deployment barriers. We have prototyped the knowledge plane and associated devices. Experience with deploying analyses over production networks demonstrate that knowledge planes impose low cost and can scale to support Internet-scale networks

Trustworthy Knowledge Planes For Federated Distributed Systems

In federated distributed systems, such as the Internet and the public cloud, the constituent systems can differ in their configuration and provisioning, resulting in significant impacts on the performance, robustness, and security of applications. Yet these systems lack support for distinguishing such characteristics, resulting in uninformed service selection and poor inter-operator coordination. This thesis presents the design and implementation of a trustworthy knowledge plane that can determine such characteristics about autonomous networks on the Internet. A knowledge plane collects the state of network devices and participants. Using this state, applications infer whether a network possesses some characteristic of interest. The knowledge plane uses attestation to attribute state descriptions to the principals that generated them, thereby making the results of inference more trustworthy. Trustworthy knowledge planes enable applications to establish stronger assumptions about their network operating environment, resulting in improved robustness and reduced deployment barriers. We have prototyped the knowledge plane and associated devices. Experience with deploying analyses over production networks demonstrate that knowledge planes impose low cost and can scale to support Internet-scale networks

Mechanistic differences in the transcriptional activation of p53 by 14-3-3 isoforms

p53 maintains genome integrity by initiating the transcription of genes involved in cell-cycle arrest, senescence, apoptosis and DNA repair. The activity of p53 is regulated by both post-translational modifications and protein–protein interactions. p53 that has been phosphorylated at S366, S378 and T387 binds 14-3-3 proteins in vitro. Here, we show that these sites are potential 14-3-3 binding sites in vivo. Epsilon (ε) and gamma (γ) isoforms required phosphorylation at either of these sites for efficient interaction with p53, while for sigma (σ) and tau (τ) these sites are dispensable. Further, σ and τ bound more weakly to p53 C-terminal phosphopeptides than did ε and γ. However, the four isoforms bound tightly to di-phosphorylated p53 C-terminal peptides than did the mono-phosphorylated counterparts. Interestingly, all the isoforms studied transcriptionally activated wild-type p53. σ and τ stabilized p53 levels in cells, while ε and γ stimulated p53-DNA binding activity in vitro. Overall, the results suggest that structurally and functionally similar 14-3-3 isoforms may exert their regulatory potential on p53 through different mechanisms. We discuss the isoform-specific roles of 14-3-3 in p53 stabilization and activation of specific-DNA binding

p53 Activation following Rift Valley Fever Virus Infection Contributes to Cell Death and Viral Production

Rift Valley fever virus (RVFV) is an emerging viral zoonosis that is responsible for devastating outbreaks among livestock and is capable of causing potentially fatal disease in humans. Studies have shown that upon infection, certain viruses have the capability of utilizing particular cellular signaling pathways to propagate viral infection. Activation of p53 is important for the DNA damage signaling cascade, initiation of apoptosis, cell cycle arrest and transcriptional regulation of multiple genes. The current study focuses on the role of p53 signaling in RVFV infection and viral replication. These results show an up-regulation of p53 phosphorylation at several serine sites after RVFV MP-12 infection that is highly dependent on the viral protein NSs. qRT-PCR data showed a transcriptional up-regulation of several p53 targeted genes involved in cell cycle and apoptosis regulation following RVFV infection. Cell viability assays demonstrate that loss of p53 results in less RVFV induced cell death. Furthermore, decreased viral titers in p53 null cells indicate that RVFV utilizes p53 to enhance viral production. Collectively, these experiments indicate that the p53 signaling pathway is utilized during RVFV infection to induce cell death and increase viral production

Newborn Sequencing in Genomic Medicine and Public Health

The rapid development of genomic sequencing technologies has decreased the cost of genetic analysis to the extent that it seems plausible that genome-scale sequencing could have widespread availability in pediatric care. Genomic sequencing provides a powerful diagnostic modality for patients who manifest symptoms of monogenic disease and an opportunity to detect health conditions before their development. However, many technical, clinical, ethical, and societal challenges should be addressed before such technology is widely deployed in pediatric practice. This article provides an overview of the Newborn Sequencing in Genomic Medicine and Public Health Consortium, which is investigating the application of genome-scale sequencing in newborns for both diagnosis and screening

Requirements for Receptor Engagement during Infection by Adenovirus Complexed with Blood Coagulation Factor X

Human adenoviruses from multiple species bind to coagulation factor X (FX), yet the importance of this interaction in adenovirus dissemination is unknown. Upon contact with blood, vectors based on adenovirus serotype 5 (Ad5) binds to FX via the hexon protein with nanomolar affinity, leading to selective uptake of the complex into the liver and spleen. The Ad5:FX complex putatively targets heparan sulfate proteoglycans (HSPGs). The aim of this study was to elucidate the specific requirements for Ad5:FX-mediated cellular uptake in this high-affinity pathway, specifically the HSPG receptor requirements as well as the role of penton base-mediated integrin engagement in subsequent internalisation. Removal of HS sidechains by enzymatic digestion or competition with highly-sulfated heparins/heparan sulfates significantly decreased FX-mediated Ad5 cell binding in vitro and ex vivo. Removal of N-linked and, in particular, O-linked sulfate groups significantly attenuated the inhibitory capabilities of heparin, while the chemical inhibition of endogenous HSPG sulfation dose-dependently reduced FX-mediated Ad5 cellular uptake. Unlike native heparin, modified heparins lacking O- or N-linked sulfate groups were unable to inhibit Ad5 accumulation in the liver 1h after intravascular administration of adenovirus. Similar results were observed in vitro using Ad5 vectors possessing mutations ablating CAR- and/or αv integrin binding, demonstrating that attachment of the Ad5:FX complex to the cell surface involves HSPG sulfation. Interestingly, Ad5 vectors ablated for αv integrin binding showed markedly delayed cell entry, highlighting the need for an efficient post-attachment internalisation signal for optimal Ad5 uptake and transport following surface binding mediated through FX. This study therefore integrates the established model of αv integrin-dependent adenoviral infection with the high-affinity FX-mediated pathway. This has important implications for mechanisms that define organ targeting following contact of human adenoviruses with blood

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Review of Kaon Physics at CERN and in Europe

The Kaon physics program at CERN and in Europe will be presented. I will first give a short review of recent results form the NA48/2 and NA62 experiments, with special emphasis to the measurement of RK , the ratio of Kaon leptonic decays rates, K → eν and K → μν, using the full minimum bias data sample collected in 2007-2008. The main subject of the talk will be the study of the highly suppressed decay K → πνν. While its rate can be predicted with minimal theoretical uncertainty in the Standard Model (BR ∼ 8 × 10−11), the smallness of BR and the challenging experimental signature make it very difficult to measure. The branching ratio for this decay is thus a sensitive probe of the flavour sector of the SM. The aim of NA62 is the measurement of the K → πνν BR with ∼ 10% precision in two years of data taking. This will require the observation of 10K decays in the experiment's fiducial volume, as well as the use of high-performance systems for precision tracking, particle identification, and photon vetoing. These aspects of the experiment will also allow NA62 to carry out a rich program of searches for lepton flavour and/or number violating K decays. Data taking will start in October 2014. The physics prospects and the status of the construction and commissioning of the NA62 experiment will be presented. In the last part of the talk I will report on Kaon physics results and prospects from other experiments at CERN (e.g. LHCb) and in Europe (e.g. KLOE and KLOE-2) and briefly mention the status in US

NetQuery: A General-Purpose Channel for Reasoning about Network

Although the configuration of modern networks has a significant impact on the performance, robustness, and security of applications, networks lack support for reporting these differences. This paper presents the design and implementation of NetQuery, a novel, general-purpose channel for disseminating the properties of networks and their participants. Net- Query implements a distributed, decentralized, tuple-based attribute store that records information about network entities. Operators can add new tuples into this store and can also annotate existing tuples with new, custom attributes, thus allowing the system to support network entities and properties not anticipated at the time of deployment. Net- Query clients can query this attribute store for the current network state and install event triggers to detect future state transitions, thus establishing long-running guarantees over the behavior of the network. We have implemented Net- Query and deployed networks with NetQuery-enabled devices that leverage commodity trusted hardware to provide strong assurance over the accuracy of reported properties. We describe the NetQuery system, outline the types of new applications enabled by NetQuery, and report on the performance of the system from deployments of real devices and from simulations of ISP networks.AFRL FA8750-07-2-003