Among other effects, post-translational modifications (PTMs) have been shown to exert their function via the modulation of protein-protein interactions. For twelve different main PTM-types and associated subtypes and across 9 diverse species, we investigated whether particular PTM-types are associated with proteins with specific and possibly “strategic” placements in the network of all protein interactions by determining informative network-theoretic properties. Proteins undergoing a PTM were observed to engage in more interactions and positioned in more central locations than non-PTM proteins. Among the twelve considered PTM-types, phosphorylated proteins were identified most consistently as being situated in central network locations and with the broadest interaction spectrum to proteins carrying other PTM-types, while glycosylated proteins are preferentially located at the network periphery. For the human interactome, proteins undergoing sumoylation or proteolytic cleavage were found with the most characteristic network properties. PTM-type-specific protein interaction network (PIN) properties can be rationalized with regard to the function of the respective PTM-carrying proteins. For example, glycosylation sites were found enriched in proteins with plasma membrane localizations and transporter or receptor activity, which generally have fewer interacting partners. The involvement in disease processes of human proteins undergoing PTMs was also found associated with characteristic PIN properties. By integrating global protein interaction networks and specific PTMs, our study offers a novel approach to unraveling the role of PTMs in cellular processes.

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The Roles of Post-translational Modifications in the Context of Protein Interaction Networks

Significance: Peroxiredoxins (Prxs) are thiol peroxidases with multiple functions in the antioxidant defense and redox signaling network of the cell. Our progressing understanding assigns both local and global significance to plant Prxs, which are grouped in four Prx types. In plants they are localized to the cytosol, mitochondrion, plastid, and nucleus. Antioxidant defense is fundamentally connected to redox signaling, cellular communication, and acclimation. The thiol–disulfide network is central part of the stress sensing and processing response and integrates information input with redox regulation. Recent Advances: Prxs function both as redox sensory system within the network and redox-dependent interactors. The processes directly or indirectly targeted by Prxs include gene expression, post-transcriptional reactions, including translation, post-translational regulation, and switching or tuning of metabolic pathways, and other cell activities. The most advanced knowledge is available for the ...

Peroxiredoxins and Redox Signaling in Plants.

Mobile malware attacks: Review, taxonomy & future directions

Protein post-translational modifications (PTMs) play a pivotal role in numerous biological processes by modulating regulation of protein function. We have developed iPTMnet (http://proteininformationresource.org/iPTMnet) for PTM knowledge discovery, employing an integrative bioinformatics approach-combining text mining, data mining, and ontological representation to capture rich PTM information, including PTM enzyme-substrate-site relationships, PTM-specific protein-protein interactions (PPIs) and PTM conservation across species. iPTMnet encompasses data from (i) our PTM-focused text mining tools, RLIMS-P and eFIP, which extract phosphorylation information from full-scale mining of PubMed abstracts and full-length articles; (ii) a set of curated databases with experimentally observed PTMs; and iii) Protein Ontology that organizes proteins and PTM proteoforms, enabling their representation, annotation and comparison within and across species. Presently covering eight major PTM types (phosphorylation, ubiquitination, acetylation, methylation, glycosylation, S-nitrosylation, sumoylation and myristoylation), iPTMnet knowledgebase contains more than 654 500 unique PTM sites in over 62 100 proteins, along with more than 1200 PTM enzymes and over 24 300 PTM enzyme-substrate-site relations. The website supports online search, browsing, retrieval and visual analysis for scientific queries. Several examples, including functional interpretation of phosphoproteomic data, demonstrate iPTMnet as a gateway for visual exploration and systematic analysis of PTM networks and conservation, thereby enabling PTM discovery and hypothesis generation.

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iPTMnet: an integrated resource for protein post-translational modification network discovery.

Plants are sessile organisms that need to respond to environmental changes quickly and efficiently. They can accomplish this by triggering specialized signaling pathways often mediated by protein phosphorylation and dephosphorylation. Phosphorylation is a fast response that can switch on or off a myriad of biological pathways and processes. Proteomics and MS are the main tools employed in the study of protein phosphorylation. Advances in the technologies allow simultaneous identification and quantification of thousands of phosphopeptides and proteins that are essential to understanding the sophisticated biological systems and regulations. In this review, we summarize the advances in phosphopeptide enrichment and quantitation, MS for phosphorylation site mapping and new data acquisition methods, databases and informatics, interpretation of biological insights and crosstalk with other PTMs, as well as future directions and challenges in the field of phosphoproteomics.

Recent advances and challenges in plant phosphoproteomics

In the past few years, the Plant Protein Phosphorylation Database (P(3)DB, http://p3db.org) has become one of the most significant in vivo data resources for studying plant phosphoproteomics. We have substantially updated P(3)DB with respect to format, new datasets and analytic tools. In the P(3)DB 3.0, there are altogether 47 923 phosphosites in 16 477 phosphoproteins curated across nine plant organisms from 32 studies, which have met our multiple quality standards for acquisition of in vivo phosphorylation site data. Centralized by these phosphorylation data, multiple related data and annotations are provided, including protein-protein interaction (PPI), gene ontology, protein tertiary structures, orthologous sequences, kinase/phosphatase classification and Kinase Client Assay (KiC Assay) data--all of which provides context for the phosphorylation event. In addition, P(3)DB 3.0 incorporates multiple network viewers for the above features, such as PPI network, kinase-substrate network, phosphatase-substrate network, and domain co-occurrence network to help study phosphorylation from a systems point of view. Furthermore, the new P(3)DB reflects a community-based design through which users can share datasets and automate data depository processes for publication purposes. Each of these new features supports the goal of making P(3)DB a comprehensive, systematic and interactive platform for phosphoproteomics research.

/pdf/p3db-3-0-from-plant-phosphorylation-sites-to-protein-144kdr4j51.pdf

P3DB 3.0: From plant phosphorylation sites to protein networks

The X.509 Public-Key Infrastructure has long been used in the SSL/TLS protocol to achieve authentication. A recent trend of Internet-of-Things (IoT) systems employing small footprint SSL/TLS libraries for secure communication has further propelled its prominence. The security guarantees provided by X.509 hinge on the assumption that the underlying implementation rigorously scrutinizes X.509 certificate chains, and accepts only the valid ones. Noncompliant implementations of X.509 can potentially lead to attacks and/or interoperability issues. In the literature, black-box fuzzing has been used to find flaws in X.509 validation implementations, fuzzing, however, cannot guarantee coverage and thus severe flaws may remain undetected. To thoroughly analyze X.509 implementations in small footprint SSL/TLS libraries, this paper takes the complementary approach of using symbolic execution. We observe that symbolic execution, a technique proven to be effective in finding software implementation flaws, can also be leveraged to expose noncompliance in X.509 implementations. Directly applying an off-the-shelf symbolic execution engine on SSL/TLS libraries is, however, not practical due to the problem of path explosion. To this end, we propose the use of SymCerts, which are X.509 certificate chains carefully constructed with a mixture of symbolic and concrete values. Utilizing SymCerts and some domain-specific optimizations, we symbolically execute the certificate chain validation code of each library and extract path constraints describing its accepting and rejecting certificate universes. These path constraints help us identify missing checks in different libraries. For exposing subtle but intricate noncompliance with X.509 standard, we cross-validate the constraints extracted from different libraries to find further implementation flaws. Our analysis of 9 small footprint X.509 implementations has uncovered 48 instances of noncompliance. Findings and suggestions provided by us have already been incorporated by developers into newer versions of their libraries.

/pdf/symcerts-practical-symbolic-execution-for-exposing-375tlx8luu.pdf

SymCerts: Practical Symbolic Execution for Exposing Noncompliance in X.509 Certificate Validation Implementations

Influence of privacy priming and security framing on mobile app selection

Android 5 informs users of all permissions requested when downloading an app and gives users an all-or-nothing acceptance decision to make for the permissions In contrast, Android 6 informs users of each permission upon first use of the downloaded app We conducted an online study with participants recruited through Amazon Mechanical Turk to compare the relative usability of the two permissions interfaces Each interface condition contained a simulation of the Google Play Store and instructed participants to role-play the task of downloading an app Afterward, each participant was questioned about which permissions were seen and the functions of those permissions The Android 5 interface showed better performance with informing users as to which permissions access their device, whereas the Android 6 interface fared better with presenting the functions of the permissions Also, the Android 6 interface was found to be more intuitive to use than that of Android 5 Although a pilot study showed that 

Cybersecurity for Android Applications: Permissions in Android 5 and 6

Despite years of research, many existing e-voting systems do not adequately protect voting privacy. In most cases, such systems only achieve "immediate privacy", that is, they only protect voting privacy against today's adversaries, but not against a future adversary, who may possess better attack technologies like new cryptanalysis algorithms and/or quantum computers. Previous attempts at providing long-term voting privacy (dubbed "everlasting privacy" in the literature) often require additional trusts in parties that do not need to be trusted for immediate privacy. In this paper, we present a framework of adversary models regarding e-voting systems, and analyze possible threats to voting privacy under each model. Based on our analysis, we argue that secret-sharing based voting protocols offer a more natural and elegant privacy-preserving solution than their encryption-based counterparts. We thus design and implement Koinonia, a voting system that provides long-term privacy against powerful adversaries and enables anyone to verify that each ballot is well-formed and the tallying is done correctly. Our experiments show that Koinonia protects voting privacy with a reasonable performance.

/pdf/koinonia-verifiable-e-voting-with-long-term-privacy-2yw0bzf5s2.pdf

Huangyi Ge

Papers

P3DB 3.0: From plant phosphorylation sites to protein networks

SymCerts: Practical Symbolic Execution for Exposing Noncompliance in X.509 Certificate Validation Implementations

Influence of privacy priming and security framing on mobile app selection

Cybersecurity for Android Applications: Permissions in Android 5 and 6

Koinonia: verifiable e-voting with long-term privacy