414 research outputs found
ICEKp2: description of an integrative and conjugative element in Klebsiella pneumoniae, co-occurring and interacting with ICEKp1
No full textKlebsiella pneumoniae is a human pathogen, prominent in antimicrobial-resistant and nosocomial
infection. The integrative and conjugative element ICEKp1 is present in a third of clinical isolates and
more prevalent in invasive disease; it provides genetic diversity and enables the spread of virulenceassociated
genes. We report a second integrative conjugative element that can co-occur with ICEKp1
in K. pneumoniae. This element, ICEKp2, is similar to the Pseudomonas aeruginosa pathogenicity
island PAPI. We identified ICEKp2 in K. pneumoniae sequence types ST11, ST258 and ST512, which
are associated with carbapenem-resistant outbreaks in China and the US, including isolates with and
without ICEKp1. ICEKp2 was competent for excision, but self-mobilisation to recipient Escherichia
coli was not detected. In an isolate with both elements, ICEKp2 positively influenced the efficiency of
plasmid mobilisation driven by ICEKp1. We propose a putative mechanism, in which a Mob2 ATPase of
ICEKp2 may contribute to the ICEKp1 conjugation machinery. Supporting this mechanism, mob2, but
not a variant with mutations in the ATPase motif, restored transfer efficiency to an ICEKp2 knockout.
This is the first demonstration of the interaction between integrative and conjugative genetic elements
in a single Gram-negative bacterium with implications for understanding evolution by horizontal gene
transfer
Rajakumar_Gowers_etal_supplementary – Supplemental material for Rapid Prototyping Platform for Saccharomyces cerevisiae Using Computer-Aided Genetic Design Enabled by Parallel Software and Workcell Platform Development
No full textSupplemental material, Rajakumar_Gowers_etal_supplementary for Rapid Prototyping Platform for Saccharomyces cerevisiae Using Computer-Aided Genetic Design Enabled by Parallel Software and Workcell Platform Development by P. D. Rajakumar, G-O. F. Gowers, L. Suckling, A. Foster, T. Ellis, R. I. Kitney, D. W. McClymont and P. S. Freemont in SLAS Technology</p
A Virulence Associated Siderophore Importer Reduces Antimicrobial Susceptibility of Klebsiella pneumoniae
No full textThe accessory genomes of many pathogenic bacteria include ABC transporters that scavenge metal by siderophore uptake and ABC transporters that contribute to antimicrobial resistance by multidrug efflux. There are mechanistic and recently recognized structural similarities between siderophore importer proteins and efflux pumps. Here we investigated the influence of siderophore importer YbtPQ on antimicrobial resistance of Klebsiella pneumoniae. YbtPQ is encoded in the yersiniabactin cluster in a prevalent mobile genetic element ICEKp, and is also common in pathogenicity islands of Escherichia coli and Yersinia species, where yersiniabactin enhances virulence. Deletion of ICEKp increased the susceptibility of K. pneumoniae to all antimicrobials tested. The mechanism was dependent on the yersiniabactin importer YbtPQ and may involve antimicrobial efflux, since it was affected by the inhibitor reserpine. The element ICEKp is naturally highly mobile, indeed the accessory genome of K. pneumoniae is recognized as a reservoir of genes for the emergence of hospital outbreak strains and for transfer to other Gram-negative pathogens. Introduction of ICEKp, or a plasmid encoding YbtPQ, to E. coli decreased its susceptibility to a broad range of antimicrobials. Thus a confirmed siderophore importer, on a rapidly evolving and highly mobile element capable of interspecies transfer, may have a secondary function exporting antimicrobials
Nexus of 6G and Blockchain for Authentication of Aerial and IoT Devices
No full textInternet of Things (IoT) is a system of interrelated sensors and computers to transfer data over a network. However, the sensors, Unmanned Aerial Vehicles (UAVs), and other IoT equipment used are susceptible to different security attacks. Dumb sensors are used to collect data in hostile environments. Dumb sensors are low powered sensors that lack computational power to perform cryptological operations. These sensors are preferred over high powered sensors due to their low electrical signature, but they have negligible computing power. To overcome the loss of authentication data due to node capture and lack of sensor location verification, we propose the Nexus of 6G and Blockchain for Authentication (NBA) system. The NBA system utilizes a permissioned blockchain-based network of UAVs and smart sensors to prevent code tampering. The system enables two-way trusted data transfer between UAVs and dumb sensors through a novel Hybrid Physical Unclonable Function Hashing (HPUFH) model. The system also utilizes a novel Pattern-based Signal Strength Correlation (PbSSC) algorithm to detect any unexpected location changes in the dumb sensor field. The extensive security and performance evaluation demonstrates that the proposed system is highly efficient and secure with a linear computational cost proportional to the number of challenge-response pairs
Supplementary Tables and Figures -Supplemental material for Associations Between the Features of Gross Placental Morphology and Birthweight
No full textSupplemental material, Supplementary Tables and Figures for Associations Between the Features of Gross Placental Morphology and Birthweight by Alexa A Freedman, Carol J Hogue, Carmen J Marsit, Augustine Rajakumar, Alicia K Smith, Robert L Goldenberg, Donald J Dudley, George R Saade, Robert M Silver, Karen J Gibbins, Barbara J Stoll, Radek Bukowski and Carolyn Drews-Botsch in Pediatric and Developmental Pathology</p
Integrase controlled excision of metal-resistance genomic islands in Acinetobacter baumannii
No full textGenomic islands (GIs) are discrete gene clusters encoding for a variety of functions including
antibiotic and heavymetal resistance, some of which are tightly associated to lineages of the core genome
phylogenetic tree. We have investigated the functions of two distinct integrase genes in the mobilization
of two metal resistant GIs, G08 and G62, of Acinetobacter baumannii. Real-time PCR demonstrated
integrase-dependent GI excision, utilizing isopropyl -D-1-thiogalactopyranoside IPTG-inducible
integrase genes in plasmid-based mini-GIs in Escherichia coli. In A. baumannii, integrase-dependent
excision of the original chromosomal GIs could be observed after mitomycin C induction. In both
E. coli plasmids and A. baumannii chromosome, the rate of excision and circularization was found to
be dependent on the expression level of the integrases. Susceptibility testing in A. baumannii strain
ATCC 17978, A424, and their respective DG62 and DG08 mutants confirmed the contribution of the
GI-encoded efflux transporters to heavy metal decreased susceptibility. In summary, the data evidenced
the functionality of two integrases in the excision and circularization of the two Acinetobacter heavy-metal
resistance GIs, G08 and G62, in E. coli, as well as when chromosomally located in their natural host.
These recombination events occur at different frequencies resulting in genome plasticity and may
participate in the spread of resistance determinants in A. baumannii
Data for: Cl atom initiated tropospheric chemistry of ethyl butyrate
No full textschematic representation of experimental techniqu
Data for: Tropospheric chemistry of ethyl tiglate initiated by Cl atoms
No full textcalculation method for experimental erro
ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes
No full textArrayOme is a new program that calculates the size of genomes represented by microarray-based probes and facilitates recognition of key bacterial strains carrying large numbers of novel genes. Protein-coding sequences (CDS) that are contigu-ous on annotated reference templates and classified as ‘Present ’ in the test strain by hybridization to microarrays are merged into ICs (ICs). These ICs are then extended to account for flanking intergenic sequences. Finally, the lengths of all extended ICs are summated to yield the ‘microarray-visualized genome (MVG) ’ size. We tested and validated ArrayOme using both experimental and in silico-generated genomic hybridization data. MVG sizing of five sequenced Escherichia coli and Shigella strains resulted in an accuracy of 97–99%, as com-pared to true genome sizes, when the comprehens-ive ShE.coli meta-array gene sequences (6239 CDS) were used for in silico hybridization analysis. How-ever, the E.coli CFT073 genome size was underesti-mated by 14 % as this meta-array lacked probes for many CFT073 CDS. ArrayOme permits rapid recog-nition of discordances between PFGE-measured genome and MVG sizes, thereby enabling high-throughput identification of strains rich in novel genes. Gene discovery studies focused on these strains will greatly facilitate characterization of the global gene pool accessible to individual bacterial species
Carnitine metabolism to trimethylamine by an unusual Rieske-type oxygenase from human microbiota
No full textDietary intake of L-carnitine can promote cardiovascular diseases in humans through microbial production of trimethylamine (TMA) and its subsequent oxidation to trimethylamine N-oxide (TMAO) by hepatic flavin-containing monooxygenases. Although our microbiota are responsible for TMA formation from carnitine, the underpinning molecular and biochemical mechanisms remain unclear. In this study, using bioinformatics approaches, we first identified a two-component Rieske-type oxygenase/reductase (CntAB) and associated gene cluster proposed to be involved in carnitine metabolism in representative genomes of the human microbiota. CntA belongs to a group of previously uncharacterized Rieske-type proteins and has an unusual "bridging" glutamate but not the aspartate residue, which is believed to facilitate inter-subunit electron transfer between the Rieske centre and the catalytic mononuclear iron centre. Using Acinetobacter baumannii as the model, we then demonstrate that cntAB is essential in carnitine degradation to TMA. Heterologous overexpression of cntAB enables Escherichia coli to produce TMA, confirming that these genes are sufficient in TMA formation. Site-directed mutagenesis experiments have confirmed that this unusual "bridging glutamate" residue in CntA is essential in catalysis and neither mutant (E205D, E205A) is able to produce TMA. Together, our study reveals the molecular and biochemical mechanisms underpinning carnitine metabolism to TMA in human microbiota and assigns the role of this novel group of Rieske-type proteins in microbial carnitine metabolism
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