Identification of Anaplasma marginale Type IV Secretion System Effector Proteins

Anaplasma marginale, an obligate intracellular alphaproteobacterium in the order Rickettsiales, is a tick-borne pathogen and the leading cause of anaplasmosis in cattle worldwide. Complete genome sequencing of A. marginale revealed that it has a type IV secretion system (T4SS). The T4SS is one of seven known types of secretion systems utilized by bacteria, with the type III and IV secretion systems particularly prevalent among pathogenic Gram-negative bacteria. The T4SS is predicted to play an important role in the invasion and pathogenesis of A. marginale by translocating effector proteins across its membrane into eukaryotic target cells. However, T4SS effector proteins have not been identified and tested in the laboratory until now.Published copyLockwood, S., D. E. Voth, K. A. Brayton, P. A. Beare, W. C. Brown, R. A. Heinzen, and S. L. Broschat, Identification of Anaplasma marginale type IV secretion system effector proteins, PLoS ONE, Vol. 6, No. 11, e7724, Nov. 2011. DOI: 10.1371/journal.pone.0027724

Novel Bypass Attack and BDD-based Tradeoff Analysis Against all Known Logic Locking Attacks

Logic locking has emerged as a promising technique for protecting gate-level semiconductor intellectual property. However, recent work has shown that such gate-level locking techniques are vulnerable to Boolean satisfiability (SAT) attacks. In order to thwart such attacks, several SAT-resistant logic locking techniques have been proposed, which minimize the discriminating ability of input patterns to rule out incorrect keys. In this work, we show that such SAT-resistant logic locking techniques have their own set of unique vulnerabilities. In particular, we propose a novel ``bypass attack that ensures the locked circuit works even when an incorrect key is applied. Such a technique makes it possible for an adversary to be oblivious to the type of SAT-resistant protection applied on the circuit, and still be able to restore the circuit to its correct functionality. We show that such a bypass attack is feasible on a wide range of benchmarks and SAT-resistant techniques, while incurring minimal run-time and area/delay overhead. Binary decision diagrams (BDDs) are utilized to analyze the proposed bypass attack and assess tradeoffs in security vs overhead of various countermeasures

Bostonia: The Boston University Alumni Magazine. Volume 9

Founded in 1900, Bostonia magazine is Boston University's main alumni publication, which covers alumni and student life, as well as university activities, events, and programs

Artificial Intelligence

Contains research objectives and reports on five research projects.Computation Center, M.I.T

Cowdria ruminantium DNA is unstable in a SuperCos1 library

A Cowdria ruminantium genomic library was constructed in a cosmid vector to serve as a source of easily accessible and pure C. ruminantium DNA for molecular genetic studies. The cosmid library contained 846 clones which were arrayed into microtitre plates. Restriction enzyme digestion patterns indicated that these clones had an average insert size of 35 kb. Probing of the arrays did not detect any bovine clones and only one of the known C. ruminantium genes, pCS20, was detected. Due to the high AT content and the fact that C. ruminantium genes are active in the Escherichia coli host, the C. ruminantium clones were unstable in the SuperCos 1 vector and most clones did not grow reproducibly. The library was contaminated with E. coli clones and these clones were maintained with greater fidelity than the C. ruminantium clones, resulting in a skewed representation over time. We have isolated seven C. ruminantium clones which we were able to serially culture reproducibly; two of these clones overlap. These clones constitute the first large regions of C. ruminantium DNA to be cloned and represent almost 10% of the C. ruminantium genome.The articles have been scanned in colour with a HP Scanjet 5590; 600dpi. Adobe Acrobat v.9 was used to OCR the text and also for the merging and conversion to the final presentation PDF-format.mn201

Engineering change in a non-deterministic FSM setting

personal or class-room use is granted without fee provided that copies are not made or distributed for profit or commercial advantage, the copyright notice, the title of the publication and its date appear, and notice is given that copying i

Software Model Checking with Explicit Scheduler and Symbolic Threads

In many practical application domains, the software is organized into a set of threads, whose activation is exclusive and controlled by a cooperative scheduling policy: threads execute, without any interruption, until they either terminate or yield the control explicitly to the scheduler. The formal verification of such software poses significant challenges. On the one side, each thread may have infinite state space, and might call for abstraction. On the other side, the scheduling policy is often important for correctness, and an approach based on abstracting the scheduler may result in loss of precision and false positives. Unfortunately, the translation of the problem into a purely sequential software model checking problem turns out to be highly inefficient for the available technologies. We propose a software model checking technique that exploits the intrinsic structure of these programs. Each thread is translated into a separate sequential program and explored symbolically with lazy abstraction, while the overall verification is orchestrated by the direct execution of the scheduler. The approach is optimized by filtering the exploration of the scheduler with the integration of partial-order reduction. The technique, called ESST (Explicit Scheduler, Symbolic Threads) has been implemented and experimentally evaluated on a significant set of benchmarks. The results demonstrate that ESST technique is way more effective than software model checking applied to the sequentialized programs, and that partial-order reduction can lead to further performance improvements.Comment: 40 pages, 10 figures, accepted for publication in journal of logical methods in computer scienc

Anaplasma marginale outer membrane protein vaccine candidates are conserved in North American and South African strains

Bovine anaplasmosis is a globally economically important tick-borne disease caused by the obligate intraerythrocytic rickettsia, Anaplasma marginale. A live Anaplasma centrale blood-based vaccine is available, but it does not protect against all A. marginale field strains and may also transmit other blood-borne pathogens. Five potential outer membrane protein (OMP) vaccine candidates have been well-characterised in A. marginale strains from the USA, however, their levels of conservation in other countries must be ascertained in order to inform their use in a vaccine with regional or global efficacy. This study assessed the amino acid variation in vaccine candidate OMPs in South African strains of A. marginale, and also compared the immunogenic properties between South African and US strains. OMP genes Am779, Am854, omp7, omp8 and omp9 were amplified and sequenced from a set of genetically diverse South African samples with different msp1α-genotypes. OMPs Am854 and Am779 were highly conserved, with 99–100 % amino acid identity, while Omp7, Omp8 and Omp9 had 79–100 % identity with US strains. As has been shown previously, Omp7–9 possess conserved N- and C- termini, a central variable region, and a highly conserved CD4 T-cell epitope, FLLVDDA(I/V)V, in the N-terminal region. Western blot analysis of recombinant OMPs indicates strong antigenic conservation between South African and US strains of A. marginale, suggesting that they are good candidates for use in a novel global vaccine cocktail, although further work on the best formulation and delivery methods will be necessary.The National Research Foundation (NRF) (Nicola Collins, grant number 81840) and Technology Innovation Agency, Tshwane Animal Health Cluster (Marinda Oosthuizen, grant number TAHC12-00037).http://www.elsevier.com/locate/ttbdis2021-04-18hj2020Veterinary Tropical Disease

The alpha 7 nicotinic receptor agonist PHA-543613 hydrochloride inhibits <i>Porphyromonas gingivalis</i>-induced expression of interleukin-8 by oral keratinocytes

Objective: The alpha 7 nicotinic receptor (α7nAChR) is expressed by oral keratinocytes. α7nAChR activation mediates anti-inflammatory responses. The objective of this study was to determine if α7nAChR activation inhibited pathogen-induced interleukin-8 (IL-8) expression by oral keratinocytes.&lt;p&gt;&lt;/p&gt; Materials and methods: Periodontal tissue expression of α7nAChR was determined by real-time PCR. OKF6/TERT-2 oral keratinocytes were exposed to &lt;i&gt;Porphyromonas gingivalis&lt;/i&gt; in the presence and absence of a α7nAChR agonist (PHA-543613 hydrochloride) alone or after pre-exposure to a specific α7nAChR antagonist (α-bungarotoxin). Interleukin-8 (IL-8) expression was measured by ELISA and real-time PCR. Phosphorylation of the NF-κB p65 subunit was determined using an NF-κB p65 profiler assay and STAT-3 activation by STAT-3 in-cell ELISA. The release of ACh from oral keratinocytes in response to &lt;i&gt;P. gingivalis&lt;/i&gt; lipopolysaccharide was determined using a GeneBLAzer M3 CHO-K1-blacell reporter assay.&lt;p&gt;&lt;/p&gt; Results: Expression of α7nAChR mRNA was elevated in diseased periodontal tissue. PHA-543613 hydrochloride inhibited &lt;i&gt;P. Gingivalis&lt;/i&gt;-induced expression of IL-8 at the transcriptional level. This effect was abolished when cells were pre-exposed to a specific α7nAChR antagonist, α-bungarotoxin. PHA-543613 hydrochloride downregulated NF-κB signalling through reduced phosphorylation of the NF-κB p65-subunit. In addition, PHA-543613 hydrochloride promoted STAT-3 signalling by maintenance of phosphorylation. Furthermore, oral keratinocytes upregulated ACh release in response to &lt;i&gt;P. Gingivalis&lt;/i&gt; lipopolysaccharide.&lt;p&gt;&lt;/p&gt; Conclusion: These data suggest that α7nAChR plays a role in regulating the innate immune responses of oral keratinocytes.&lt;p&gt;&lt;/p&gt

Colloidal suspensions in modulated light fields

Periodically-modulated potentials in the form of light fields have previously been applied to induce reversible phase transitions in dilute colloidal systems with long-range interactions. Here we investigate whether similar transitions can be induced in very dense systems, where inter-particle contacts are important. Using microscopy we show that particles in such systems are indeed strongly affected by modulated potentials. We discuss technical aspects relevant to generating the light-induced potentials and to imaging simultaneously the particles. We also consider what happens when the particle size is comparable with the modulation wavelength. The effects of selected modulation wavelengths as well as pure radiation pressure are illustrated.Comment: Accepted by J. Phys.: Condens. Matter, CODEF II Special Issue. 23 pages, 12 figure