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The bacterial wilt pathogenRalstonia pseudosolanacearum (Rps)colonizes plant xylem vessels and blocks the flow of xylem sap by its biofilm (comprising of bacterial cells and extracellular material), resulting in devastating wilt disease across many economically important host plants including tomatoes. The technical challenges of imaging the xylem environment, along with the use of artificial cell culture plates and media in existingin vitrosystems, limit the understanding ofRpsbiofilm formation and its infection dynamics. In this study, we designed and built a microfluidic system that mimicked the physical and chemical conditions of the tomato xylem vessels, and allowed us to dissectRpsresponses to different xylem-like conditions. The system, incorporating functional surface coatings of carboxymethyl cellulose-dopamine, provided a bioactive environment that significantly enhancedRpsattachment and biofilm formation in the presence of tomato xylem sap. Using computational approaches, we confirmed thatRpsexperienced linear increasing drag forces in xylem-mimicking channels at higher flow rates. Consistently, attachment and biofilm assays conducted in our microfluidic system revealed that both seeding time and flow rates were critical for bacterial adhesion to surface and biofilm formation inside the channels. These findings provided insights into theRpsattachment and biofilm formation processes, contributing to a better understanding of plant-pathogen interactions during wilt disease development. 

Microsporidia are a large phylum of intracellular parasites that can infect most types of animals. Species in theNematocidagenus can infect nematodes includingCaenorhabditis elegans, which has become an important model to study mechanisms of microsporidia infection. To understand the genomic properties and evolution of nematode-infecting microsporidia, we sequenced the genomes of nine species of microsporidia, including two genera,EnteropsectraandPancytospora, without any previously sequenced genomes. Core cellular processes, including metabolic pathways, are mostly conserved across genera of nematode-infecting microsporidia. Each species encodes unique proteins belonging to large gene families that are likely used to interact with host cells. Most strikingly, we observed one such family, NemLGF1, is present in bothNematocidaandPancytosporaspecies, but not any other microsporidia. To understand howNematocidaphenotypic traits evolved, we measured the host range, tissue specificity, spore size, and polar tube length of several species in the genus. Our phylogenetic analysis shows thatNematocidais composed of two groups of species with distinct traits and that species with longer polar tubes infect multiple tissues. Together, our work details both genomic and trait evolution between related microsporidia species and provides a useful resource for further understanding microsporidia evolution and infection mechanisms. 

Byzantine Fault Tolerant (BFT) protocols are designed to ensure correctness and eventual progress in the face of misbehaving nodes [1]. However, this does not prevent negative effects an adversary may have on performance: a faulty node may significantly affect the latency and throughput of the system without being detected. This is especially true in speculative protocols optimized for the best-case where a single leader can force the protocol into the worst case [3]. Systems like Aardvark [2] that are designed to maximize worst-case performance tolerate byzantine behavior without necessarily detecting who the perpetrator is. By forcing regular view changes, for example, they mitigate the effects of leaders who deliberately delay dissemination of messages, even if this behavior would be difficult to prove to a third party. Byzantine faults, by definition, can be difficult to detect. An error of 'commission', such as a message with a mismatching digest, can be proven. Errors of 'omission', such as delaying or failing to relay a message, as a rule cannot be proven, and the node responsible for these types of omission faults may not appear faulty to all observers. Nevertheless, we observe that they can reliably be detected. Designing protocols that detect and eject nodes is challenging for two reasons. First, some behaviors are observed by a subset of honest nodes and cannot be objectively proven to a third party. Second, any mechanism capable of ejecting nodes could be subverted by Byzantine nodes to eject honest nodes. This paper presents the Protocol for Ejecting All Corrupted Hosts (Peach, a mechanism for detecting and ejecting faulty nodes in Byzantine fault tolerant (BFT) protocols. Nodes submit votes to a trusted configuration manager that replaces faulty nodes once a threshold of votes are received. We implement Peach for two BFT protocol variants, a traditional pbft-style three-phase protocol and a speculative protocol, and evaluate its ability to respond to Byzantine behavior. This work makes the following contributions: (1) We present and prove a necessary and sufficient constraint on cluster membership guaranteeing that any nodes causing performance degradation via acts of omission will be detected. (2) We present an agreement protocol, PEACHes, in which replicas pass votes about their subjective local observations of possible omissions to a TTP. (3) We show how the separation of detection and effectuation allows fine-grained detection of malicious behavior that is compatible and easily integrated with existing systems. (4) We present DecentBFT, an extension of BFT-Smart to which we added a speculative fast path (similar to Zyzzva) and integrated PEACHes. (5) We show DecentBFT rapidly detects and mitigates a variety of performance attacks that would have gone undetected by the state of the art. 

ABSTRACT SalmonellaOuter Membrane Vesicles (OMVs) were recently shown to inhibit P22 bacteriophage infection. Furthermore, despite there being several published reports now independently describing (1) the marked prevalence of tRFs within secreted vesicle transcriptomes and (2) roles for specific tRFs in facilitating/inhibiting viral replication, there have been no examinations of the effects of vesicle-secreted tRFs on viral infection reported to date. Notably, while specific tRFs have been reported in a number of bacteria, the tRFs expressed by salmonellae have not been previously characterized. As such, we recently screened small RNA-seq datasets for the presence of recurrent, specifically excised tRFs and identified 31 recurrent, relatively abundant tRFs expressed bySalmonella entericaserovar Typhimurium (SL1344). What’s more, we findS. Typhimurium OMVs contain significant levels of tRFs highly complementary to knownSalmonella enterica-infecting bacteriophage with 17 of 31 tRFs bearing marked complementarity to at least one knownSalmonella enterica-infecting phage (averaging 97.4% complementarity over 22.9 nt). Most notably, tRNA-Thr-CGT-1-1, 44-73, bears 100% sequence complementary over its entire 30 nt length to 29 distinct, annotatedSalmonella enterica-infecting bacteriophage including P22. Importantly, we find inhibiting this tRF in secreted OMVs improves P22 infectivity in a dose dependent manner whereas raising OMV tRF levels conversely inhibits P22 infectivity. Furthermore, we find P22 phage pre-incubation with OMVs isolated from naïve, control SL1344S. Typhimurium, successfully rescues the ability ofS. Typhimurium transformed with a specific tRNA-Thr-CGT-1-1, 44-73 tRF inhibitor to defend against P22. Collectively, these experiments confirm tRFs secreted inS. Typhimurium OMVs are directly involved with and required for the ability of OMVs to defend against bacteriophage predation. As we find the majority of OMV tRFs are highly complementary to an array of knownSalmonella enterica-infecting bacteriophage, we suggest OMV tRFs may primarily function as a broadly acting, previously uncharacterized innate antiviral defense.