92 research outputs found

    Structure of a translocation signal domain mediating conjugative transfer by Type IV secretion systems

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    Relaxases are proteins responsible for the transfer of plasmid and chromosomal DNA from one bacterium to another during conjugation. They covalently react with a specific phosphodiester bond within DNA origin of transfer sequences, forming a nucleo-protein complex which is subsequently recruited for transport by a plasmid-encoded type IV secretion system. In previous work we identified the targeting translocation signals presented by the conjugative relaxase TraI of plasmid R1. Here we report the structure of TraI translocation signal TSA. In contrast to known translocation signals we show that TSA is an independent folding unit and thus forms a bona fide structural domain. This domain can be further divided into three sub-domains with striking structural homology with helicase sub-domains of the SF1B family. We also show that TSA is part of a larger vestigial helicase domain which has lost its helicase activity but not its single-stranded DNA binding capability. Finally, we further delineate the binding site responsible for translocation activity of TSA by targeting single residues for mutations. Overall, this study provides the first evidence that translocation signals can be part of larger structural scaffolds, overlapping with translocation-independent activities

    Silencing hardware backdoors.

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    Abstract-Hardware components can contain hidden backdoors, which can be enabled with catastrophic effects or for ill-gotten profit. These backdoors can be inserted by a malicious insider on the design team or a third-party IP provider. In this paper, we propose techniques that allow us to build trustworthy hardware systems from components designed by untrusted designers or procured from untrusted third-party IP providers. We present the first solution for disabling digital, designlevel hardware backdoors. The principle is that rather than try to discover the malicious logic in the design -an extremely hard problem -we make the backdoor design problem itself intractable to the attacker. The key idea is to scramble inputs that are supplied to the hardware units at runtime, making it infeasible for malicious components to acquire the information they need to perform malicious actions. We show that the proposed techniques cover the attack space of deterministic, digital HDL backdoors, provide probabilistic security guarantees, and can be applied to a wide variety of hardware components. Our evaluation with the SPEC 2006 benchmarks shows negligible performance loss (less than 1% on average) and that our techniques can be integrated into contemporary microprocessor designs

    Clinical Efficacy of Romidepsin in Tumor Stage and Folliculotropic Mycosis Fungoides

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    AbstractBackgroundTumor stage and folliculotropic mycosis fungoides are uncommon subtypes of cutaneous T-cell lymphoma (CTCL) with an aggressive disease course. Romidepsin is a histone deacetylase inhibitor approved by the US Food and Drug Administration for patients with CTCL who have received ≄ 1 previous systemic therapy. In the present study, we examined the efficacy and safety of romidepsin in patients from the pivotal, single-arm, open-label, phase II study of relapsed or refractory CTCL with cutaneous tumors and/or folliculotropic disease involvement.Materials and MethodsPatients with CTCL who had received ≄ 1 previous systemic therapy received romidepsin at 14 mg/m2 on days 1, 8, and 15 of 28-day cycles. Responses were determined by a composite endpoint (assessments of the skin, blood, and lymph nodes). Patients with cutaneous tumors and/or folliculotropic disease involvement were identified by review of diagnosis and histology reports.ResultsThe objective response rate to romidepsin was 45% in patients with cutaneous tumors (n = 20) and 60% in patients with folliculotropic disease involvement (n = 10).ConclusionRomidepsin is active in subtypes of CTCL with less favorable outcomes, such as tumor stage and folliculotropic mycosis fungoides

    A Red Team/Blue Team Assessment of Functional Analysis Methods for Malicious Circuit Identification

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    Recent advances in hardware security have led to the development of FANCI (Functional Analysis for Nearly-Unused Circuit Identification), an analysis tool that identifies stealthy, malicious circuits within hardware designs that can perform malicious backdoor behavior. Evaluations of such tools against benchmarks and academic attacks are not always equivalent to the dynamic attack scenarios that can arise in the real world. For this reason, we apply a red team/blue team approach to stress-test FANCI's abilities to efficiently detect malicious backdoor circuits within hardware designs. In the Embedded Systems Challenge (ESC) 2013, teams from research groups from multiple continents created designs with malicious backdoors hidden in them as part of a red team effort to circumvent FANCI. Notably, these backdoors were not placed into a priori known designs. The red team was allowed to create arbitrary, unspecified designs. Two interesting results came out of this effort. The first was that FANCI was surprisingly resilient to this wide variety of attacks and was not circumvented by any of the stealthy backdoors created by the red teams. The second result is that frequent-action backdoors, which are backdoors that are not made stealthy, were often successful. These results emphasize the importance of combining FANCI with a reasonable degree of validation testing. The blue team efforts also exposed some aspects of the FANCI prototype that make analysis time-consuming in some cases, which motivates further development of the prototype in the future

    Structure of a VirD4 coupling protein bound to a VirB type IV secretion machinery.

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    Type IV secretion (T4S) systems are versatile bacterial secretion systems mediating transport of protein and/or DNA T4S systems are generally composed of 11 VirB proteins and 1 VirD protein (VirD4). The VirB1-11 proteins assemble to form a secretion machinery and a pilus while the VirD4 protein is responsible for substrate recruitment. The structure of VirD4 in isolation is known; however, its structure bound to the VirB1-11 apparatus has not been determined. Here, we purify a T4S system with VirD4 bound, define the biochemical requirements for complex formation and describe the protein-protein interaction network in which VirD4 is involved. We also solve the structure of this complex by negative stain electron microscopy, demonstrating that two copies of VirD4 dimers locate on both sides of the apparatus, in between the VirB4 ATPases. Given the central role of VirD4 in type IV secretion, our study provides mechanistic insights on a process that mediates the dangerous spread of antibiotic resistance genes among bacterial populations

    Structure of a Chaperone-Usher Pilus reveals the molecular basis of rod uncoiling

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    Types 1 and P pili are prototypical bacterial cell-surface appendages playing essential roles in mediating adhesion of bacteria to the urinary tract. These pili, assembled by the chaperone-usher pathway, are polymers of pilus subunits assembling into two parts: a thin, short tip fibrillum at the top, mounted on a long pilus rod. The rod adopts a helical quaternary structure and is thought to play essential roles: its formation may drive pilus extrusion by preventing backsliding of the nascent growing pilus within the secretion pore; the rod also has striking spring-like properties, being able to uncoil and recoil depending on the intensity of shear forces generated by urine flow. Here, we present an atomic model of the P pilus generated from a 3.8 Å resolution cryo-electron microscopy reconstruction. This structure provides the molecular basis for the rod’s remarkable mechanical properties and illuminates its role in pilus secretion

    BASILICA Trial: One-Year Outcomes of Transcatheter Electrosurgical Leaflet Laceration to Prevent TAVR Coronary Obstruction

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    Background: Coronary artery obstruction is a rare, devastating complication of transcatheter aortic valve replacement. Transcatheter electrosurgical aortic leaflet laceration (Bioprosthetic or Native Aortic Scallop Intentional Laceration to Prevent Iatrogenic Coronary Artery Obstruction [BASILICA]) is a novel technique to prevent coronary artery obstruction. We report the 1-year outcomes of the BASILICA trial. Primary end points of 30-day success and safety have been reported previously. Methods: The BASILICA trial was a prospective, multicenter, single-arm safety and feasibility study. Subjects with severe native or bioprosthetic aortic valve disease at high or extreme risk for surgery, and high risk of coronary artery obstruction, were included. End points at 1 year included death, stroke, and myocardial infarction. Source data was independently verified and end points independently adjudicated. Results: Thirty subjects were enrolled between February 2018 and July 2018. At 30 days, BASILICA was successful in 28 subjects (93.3%), there were 3 strokes (10%), including 1 disabling stroke (3.3%), 1 death (3.3%), and 1 periprocedural myocardial infarction (3.3%). Between 30 days and 1 year, there were no additional strokes, no myocardial infarction, and 2 deaths (10% 1-year mortality). No subject needed repeat intervention for aortic valve or coronary disease. Two subjects had infective endocarditis (6.7%), but neither was isolated to the aortic valve. There were no hospital admissions for heart failure. Fourteen (46.7%) subjects required repeat hospital admission for other causes. Aortic valve gradients on echocardiography, New York Heart Association functional class, and Kansas City Cardiomyopathy Questionnaire scores improved from baseline to 30 days and were maintained at 1 year. Conclusions: In these subjects with multiple comorbidities and restrictive anatomy that underwent transcatheter aortic valve replacement, there was no late stroke, myocardial infarction, or death related to BASILICA. Mitigation of coronary obstruction remained intact at 1 year and was not related to recurrent readmission. These results are reassuring for patients and physicians who wish to avoid the long-term complications related to snorkel stenting
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