Acetylation of the NS3 helicase by KAT5γ is essential for flavivirus replication.

Direct targeting of essential viral enzymes such as proteases, polymerases, and helicases has long been the major focus of antiviral drug design. Although successful for some viral enzymes, targeting viral helicases is notoriously difficult to achieve, demanding alternative strategies. Here, we show that the NS3 helicase of Zika virus (ZIKV) undergoes acetylation in its RNA-binding tunnel. Regulation of the acetylated state of K389 in ZIKV NS3 modulates RNA binding and unwinding and is required for efficient viral replication. NS3 acetylation is mediated by a specific isoform of the host acetyltransferase KAT5 (KAT5γ), which translocates from the nucleus to viral replication complexes upon infection. NS3 acetylation by KAT5γ and its proviral role are also conserved in West Nile virus (WNV), dengue virus (DENV), and yellow fever virus (YFV). Our study provides molecular insight into how a cellular acetyltransferase regulates viral helicase functions, unveiling a previously unknown target for antiviral drug development.

The Changes in Epidemiology of Imipenem-Resistant Acinetobacter baumannii Bacteremia in a Pediatric Intensive Care Unit for 17 Years.

BACKGROUND: Acinetobacter baumannii infections cause high morbidity and mortality in intensive care unit (ICU) patients. However, there are limited data on the changes of long-term epidemiology of imipenem resistance in A. baumannii bacteremia among pediatric ICU (PICU) patients. METHODS: A retrospective review was performed on patients with A. baumannii bacteremia in PICU of a tertiary teaching hospital from 2000 to 2016. Antimicrobial susceptibility tests, multilocus sequence typing (MLST), and polymerase chain reaction for antimicrobial resistance genes were performed for available isolates. RESULTS: A. baumannii bacteremia occurred in 27 patients; imipenem-sensitive A. baumannii (ISAB, n = 10, 37%) and imipenem-resistant A. baumannii (IRAB, n = 17, 63%). There was a clear shift in the antibiogram of A. baumannii during the study period. From 2000 to 2003, all isolates were ISAB (n = 6). From 2005 to 2008, both IRAB (n = 5) and ISAB (n = 4) were isolated. However, from 2009, all isolates were IRAB (n = 12). Ten isolates were available for additional test and confirmed as IRAB. MLST analysis showed that among 10 isolates, sequence type 138 was predominant (n = 7). All 10 isolates were positive for OXA-23-like and OXA-51-like carbapenemase. Of 27 bacteremia patients, 11 were male (41%), the median age at bacteremia onset was 5.2 years (range, 0-18.6 years). In 33% (9/27) of patients, A. baumannii was isolated from tracheal aspirate prior to development of bacteremia (median, 8 days; range, 5-124 days). The overall case-fatality rate was 63% (17/27) within 28 days. There was no statistical difference in the case fatality rate between ISAB and IRAB groups (50% vs. 71%; P = 0.422). CONCLUSION: IRAB bacteremia causes serious threat in patients in PICU. Proactive infection control measures and antimicrobial stewardship are crucial for managing IRAB infection in PICU.

Effect of multiple, compatible plasmids on the fitness of the bacterial host by inducing transcriptional changes.

OBJECTIVES: Bacteria that acquire plasmids incur a biological cost. Despite this fact, clinical Enterobacteriaceae isolates commonly contain multiple co-existing plasmids harbouring carbapenemase genes. METHODS: Six different plasmids carrying blaNDM-1, blaNDM-5, blaCTX-M-15, blaKPC-2, blaOXA-181 and blaOXA-232 genes were obtained from Klebsiella pneumoniae and Escherichia coli clinical isolates. Using the E. coli DH5α strain as recipient, 14 transconjugants with diverse plasmid combinations (single or double plasmids) were generated. For each of these, the effects of plasmid carriage on the bacterial host were investigated using in vitro and in vivo competition assays; additionally, the effects were investigated in the context of biofilm formation, serum resistance and survival inside macrophages. Transcriptomic changes in single- and double-plasmid recipients were also investigated. RESULTS: Increased in vitro and in vivo competitiveness was observed when two plasmids carrying blaNDM-1 and blaOXA-232 were co-introduced into the host bacteria. However, DH5α::pNDM5 + pOXA232 and other double-plasmid recipients did not show such competitiveness. DH5α::pNDM5 + pOXA181 did not show any fitness cost compared with a plasmid-free host and single-plasmid transconjugants, while both the double-plasmid recipients with pCTXM15 or pKPC2 exhibited a fitness burden. The double-plasmid recipient DH5α::pNDM1 + pOXA232 also exhibited increased biofilm formation, serum resistance and survival inside macrophages. Transcriptomic analysis revealed that the genes of DH5α::pNDM1 + pOXA232 involved in metabolic pathways, transport and stress response were up-regulated, while those involved in translation were down-regulated. CONCLUSIONS: Our study suggests that bacterial strains can gain fitness through the acquisition of multiple plasmids harbouring antibiotic resistance genes, which may be mediated by transcriptomic changes in the chromosomal genes of the bacterial host.

Change of Hypermucoviscosity in the Development of Tigecycline Resistance in Hypervirulent Klebsiella pneumoniae Sequence Type 23 Strains.

In this study, we developed tigecycline resistance in Klebsiella pneumoniae ST23 strains in vitro and investigated the change in virulence associated with hypermucoviscosity. In vitro-induced tigecycline-resistant (TGC-IR) K. pneumoniae mutants were obtained from three tigecycline-susceptible (TGC-S) strains, belonging to ST23 and serotype K1, by culturing in media with tigecycline in a stepwise manner. An antimicrobial susceptibility test, string test, mucoviscosity assay, and capsular polysaccharide (CPS) quantification were performed. Biofilm formation and serum resistance were evaluated, and survival rates of bacterial strains in fruit flies and macrophages were measured. Alterations of rpsJ, ramR, soxR, acrR, and marR genes were investigated and the expression levels of ramA and efflux pump genes were evaluated. The hypermucoviscosity phenotype was dramatically decreased in the TGC-IR mutants. Reduced CPS production in TGC-IR mutants was also identified. Increased resistance to most other antimicrobial agents was found in TGC-IR mutants. In addition, the TGC-IR mutants exhibited reduced biofilm formation, low serum resistance, and decreased survival rates within fruit flies and macrophages. Our study shows that development of tigecycline resistance in hypervirulent K. pneumoniae strains result in defects in virulence associated with hypermucoviscosity.

Position-specific oxidation of miR-1 encodes cardiac hypertrophy.

In pathophysiology, reactive oxygen species oxidize biomolecules that contribute to disease phenotypes1. One such modification, 8-oxoguanine2 (o8G), is abundant in RNA3 but its epitranscriptional role has not been investigated for microRNAs (miRNAs). Here we specifically sequence oxidized miRNAs in a rat model of the redox-associated condition cardiac hypertrophy4. We find that position-specific o8G modifications are generated in seed regions (positions 2-8) of selective miRNAs, and function to regulate other mRNAs through o8G•A base pairing. o8G is induced predominantly at position 7 of miR-1 (7o8G-miR-1) by treatment with an adrenergic agonist. Introducing 7o8G-miR-1 or 7U-miR-1 (in which G at position 7 is substituted with U) alone is sufficient to cause cardiac hypertrophy in mice, and the mRNA targets of o8G-miR-1 function in affected phenotypes; the specific inhibition of 7o8G-miR-1 in mouse cardiomyocytes was found to attenuate cardiac hypertrophy. o8G-miR-1 is also implicated in patients with cardiomyopathy. Our findings show that the position-specific oxidation of miRNAs could serve as an epitranscriptional mechanism to coordinate pathophysiological redox-mediated gene expression.

Comparison of Fitness Cost and Virulence in Chromosome- and Plasmid-Mediated Colistin-Resistant Escherichia coli.

Five types of Escherichia coli strains were obtained and sequenced: colistin-susceptible (CL-S) strains, in vitro induced colistin-resistant (CL-IR) strains, mcr-1-negative colistin-resistant strains from livestock (CL-chrR), mcr-1-positive colistin-resistant strains (CL-mcrR), and mcr-1-transferred transconjugants (TC-mcr). Amino acid alterations of PmrAB, PhoPQ, and EptA were identified, and their mRNA expression was measured. Their growth rate was evaluated, and an in vitro competition assay was performed. Virulence was compared through serum resistance and survival in macrophages and Drosophila melanogaster. CL-IR and CL-chrR strains were colistin-resistant due to amino acid alterations in PmrAB, PhoPQ, or EptA, and their overexpression. All colistin-resistant strains did not show reduced growth rates compared with CL-S strains. CL-IR and CL-chrR strains were less competitive than the susceptible strain, but CL-mcrR strains were not. In addition, TC-mcr strains were also significantly more competitive than their respective parental susceptible strain. CL-IR strains had similar or decreased survival rates in human serum, macrophages, and fruit flies, compared with their parental, susceptible strains. CL-chrR strains were also less virulent than CL-S strains. Although CL-mcrR strains showed similar survival rates in human serum and fruit fly to CL-S strains, the survival rates of TC-mcr strains decreased significantly in human serum, macrophages, and fruit flies, compared with their susceptible recipient strain (J53). Chromosome-mediated, colistin-resistant E. coli strains have a fitness cost, but plasmids bearing mcr-1 do not increase the fitness burden of E. coli. Along with high usage of polymyxins, the no fitness cost of mcr-1-positive strains may facilitate rapid spread of colistin resistance.

Co-introduction of plasmids harbouring the carbapenemase genes, blaNDM-1 and blaOXA-232, increases fitness and virulence of bacterial host.

BACKGROUND: Bacterial isolates with multiple plasmids harbouring different carbapenemase genes have emerged and been identified repeatedly, despite a general notion that plasmids confer fitness cost in bacterial host. In this study, we investigated the effects of plasmids with carbapenemase genes on the fitness and virulence of bacteria. METHODS: Different plasmids harbouring the carbapenemase genes, blaNDM-1 and blaOXA-232, were isolated from a carbapenem-resistant K. pneumoniae strain. Each plasmid was conjugated into the Escherichia coli strain DH5α, and a transconjugant with both plasmids was also obtained by transformation. Their in vitro competitive ability, biofilm formation, serum resistance, survival ability within macrophage and fruit fly, and fly killing ability were evaluated. RESULTS: The transconjugants with a single plasmid showed identical phenotypes to the plasmid-free strain, except that they decreased fly survival after infection. However, significantly increased fitness, virulence and biofilm production were observed consistently for the transconjugant with both plasmids, harbouring blaNDM-1 and blaOXA-232. CONCLUSIONS: Our data indicate that bacteria carrying multiple plasmids encoding different carbapenemases may have increased fitness and virulence, emphasizing the need for diverse strategies to combat antimicrobial resistance.

Evolution of Klebsiella pneumoniae with mucoid and non-mucoid type colonies within a single patient.

We obtained nine Klebsiella pneumoniae isolates successively isolated from a single patient. Four pairs (M1-M4 and NM1-NM4) obtained simultaneously from the same site showed different colony types, mucoid and non-mucoid, while the final isolate (M5) was isolated alone from the blood and showed a mucoid phenotype. The whole genome of isolate M5 was sequenced de novo using the PacBio RSII system, while the others were sequenced with an Illumina Hiseq4000 and mapped to the genome sequences of M5. To identify insertions or deletions in the cps locus, we amplified and sequenced cps locus genes. We identified insertion sequence (IS) elements in several genes of the cps locus or one amino acid substitution in WcaJ in all non-mucoid isolates. Five additional amino acid alterations in RpsJ, LolE, Lon-2, PpsE, and a hypothetical protein were detected in some mucoid and non-mucoid isolates. Based on the genome data and cps locus sequences, the mucoid phenotype may have been lost or converted into the non-mucoid phenotype because of the insertion of IS elements or amino acid alterations at this locus. We inferred a within-host evolutionary scenario, in which non-mucoid variants emerged repeatedly from mucoid isolates, but may be short-lived because of their low fitness.

Comparison of virulence between matt and mucoid colonies of Klebsiella pneumoniae coproducing NDM-1 and OXA-232 isolated from a single patient.

Nine Klebsiella pneumoniae isolates coproducing NDM-1 and OXA-232 carbapenemases were successively isolated from a single patient. Although they were isolated simultaneously and were isogenic, they presented different colony phenotypes (matt and mucoid). All nine isolates were resistant to most antibiotics except colistin and fosfomycin. In addition, matt-type isolates were resistant to tigecycline. No differences were detected in the cps cluster sequences, except for the insertion of IS5 in the wzb gene of two matt-type isolates. In vitro virulence assays based on production of capsular polysaccharide, biofilm formation, and resistance to human serum indicated that the mucoid-type isolates were significantly more virulent than the matt-type. In addition, mucoid-type isolates showed higher survival rates than the matt-type ones in infection experiments in the fruit fly, suggesting a higher virulence of K. pneumoniae isolates with a mucoid phenotype. To our knowledge, this is the first report of K. pneumoniae colonies with different phenotypes being isolated from the same sample. In addition, we show that virulence varies with colony phenotype. Dissemination of K. pneumoniae isolates expressing both antibiotic resistance and high virulence would constitute a great threat.

Protective effect of ginsenoside Rb1 against tacrolimus-induced apoptosis in renal proximal tubular LLC-PK1 cells.

BACKGROUND: The aim of the present study was to evaluate the potential protective effects of six ginsenosides (Rb1, Rb2, Rc, Rd, Rg1, and Rg3) isolated from Panax ginseng against tacrolimus (FK506)-induced apoptosis in renal proximal tubular LLC-PK1 cells. METHODS: LLC-PK1 cells were treated with FK506 and ginsenosides, and cell viability was measured. Protein expressions of mitogen-activated protein kinases, caspase-3, and kidney injury molecule-1 (KIM-1) were evaluated by Western blotting analyses. The number of apoptotic cells was measured using an image-based cytometric assay. RESULTS: Reduction in cell viability by 60µM FK506 was ameliorated significantly by cotreatment with ginsenosides Rg1 and Rb1. The phosphorylation of p38, extracellular signal-regulated kinases, and KIM-1, and cleavage of caspase-3, increased markedly in LLC-PK1 cells treated with FK506 and significantly decreased after cotreatment with ginsenoside Rb1. The number of apoptotic cells decreased by 6.0% after cotreatment with ginsenoside Rb1 (10µM and 50µM). CONCLUSION: The antiapoptotic effects of ginsenoside Rb1 on FK506-induced apoptosis were mediated by the inhibition of mitogen-activated protein kinases and caspase activation.

Evaluation and control of miRNA-like off-target repression for RNA interference.

RNA interference (RNAi) has been widely adopted to repress specific gene expression and is easily achieved by designing small interfering RNAs (siRNAs) with perfect sequence complementarity to the intended target mRNAs. Although siRNAs direct Argonaute (Ago), a core component of the RNA-induced silencing complex (RISC), to recognize and silence target mRNAs, they also inevitably function as microRNAs (miRNAs) and suppress hundreds of off-targets. Such miRNA-like off-target repression is potentially detrimental, resulting in unwanted toxicity and phenotypes. Despite early recognition of the severity of miRNA-like off-target repression, this effect has often been overlooked because of difficulties in recognizing and avoiding off-targets. However, recent advances in genome-wide methods and knowledge of Ago-miRNA target interactions have set the stage for properly evaluating and controlling miRNA-like off-target repression. Here, we describe the intrinsic problems of miRNA-like off-target effects caused by canonical and noncanonical interactions. We particularly focus on various genome-wide approaches and chemical modifications for the evaluation and prevention of off-target repression to facilitate the use of RNAi with secured specificity.

Microbiological features and clinical impact of the type VI secretion system (T6SS) in Acinetobacter baumannii isolates causing bacteremia.

We investigated the genetic background and microbiological features of T6SS-positive Acinetobacter baumannii isolates and clinical impact of the T6SS in patients with A. baumannii bacteremia. One hundred and 62 A. baumannii isolates from patients with bacteremia in 2 tertiary-care hospitals in Korea were included in this study. Approximately one-third (51/162, 31.5%) of the A. baumannii clinical isolates possessed the hcp gene, and the hcp-positive isolates were found in several genotypes in multilocus sequence typing. The expression and secretion of Hcp protein varied among the clinical isolates. A. baumannii isolates with detectable Hcp secretion (T6SS+) could better outcompete Escherichia coli compared with T6SS- isolates, including hcp-negative and inactivated hcp-positive isolates. In addition, T6SS+ isolates showed higher biofilm-forming activity and better survival in the presence of normal human serum than the T6SS- isolates. T6SS+ isolates were more frequently detected in patients with catheter-related bloodstream infection, haematopoietic stem cell transplant recipients, and patients receiving immunosuppressive agents. However, T6SS was not a prognostic factor for mortality. Our results suggest that the T6SS of A. baumannii is associated with virulence and contributes to infections in immunocompromised patients and those with implanted medical devices.

High prevalence of non-clonal imipenem-nonsusceptible Enterobacter spp. isolates in Korea and their association with porin down-regulation.

We investigated the prevalence and clonal distribution of imipenem-nonsusceptible Enterobacter clinical isolates from hospitals in Korea and the contributions of various mechanisms to imipenem nonsusceptibility. The in vitro antimicrobial susceptibility to imipenem of 357 non-duplicated Enterobacter isolates obtained from eight geographically distant tertiary care hospitals in Korea was evaluated. Imipenem-nonsusceptible Enterobacter isolates were genotyped. Additionally, ß-lactamase genes were screened using PCR, and the expression of efflux pump and porin genes was investigated using quantitative RT-PCR. A total of 31 isolates (8.7%) were not susceptible to imipenem. Clonal diversity of 17 imipenem-nonsusceptible E. cloacae isolates was demonstrated by multilocus sequence typing. Fourteen imipenem-nonsusceptible E. aerogenes isolates were found to be distantly genetically related by an ERIC-PCR analysis. Expression levels of porin ompD and ompK35 genes were decreased in all imipenem-nonsusceptible E. cloacae and E. aerogenes isolates. However, only two isolates were found positive for blaIMP and blaVIM genes, and expression of the efflux pump gene, acrB, was not associated with reduced imipenem susceptibility. Imipenem resistance seems to have occurred independently in most of the imipenem-nonsusceptible isolates in this study, and decreased porin expression was found to be the main mechanism underlying this reduced susceptibility to imipenem.

Morphology Control of Poly(styrene-block-dimethylsiloxane) by Simple Blending with Trimethylsilylated Silicate Nanoparticles.

Trimethylsilylated silicate nanoparticle (termed MQ resin, combining M Me3SiO1/2 and Q SiO4/2 units)/poly(styrene-block-polydimethylsiloxane) (PS-PDMS, 31K-15K, polydispersity PD = 1.15, weight-average molecular weight Mw = 45.5K) blends behave similarly to block copolymers with different PS/PDMS ratios. MQ is localized in the PDMS phase virtually extending the volume fraction in the block copolymer. This allows for microdomain morphology control beyond what can be achieved with the starting block copolymer. Synthesizing siloxane-containing block copolymers targeted at certain equilibrium morphologies can be time-consuming and in some cases technically challenging. This work shows that MQ is a robust morphology modifier, not limited by the occurrence of surface segregation and the high diffusion rates typically associated with homopolymer modification, as confirmed by looking at the PDMS/PS-PDMS reference. The convenient and robust structure control MQ nanoparticle modification of PS-PDMS provides could overcome one of the hurdles to adoption of block copolymer lithography.

Lysophosphatidylcholine activates adipocyte glucose uptake and lowers blood glucose levels in murine models of diabetes.

Glucose homeostasis is maintained by the orchestration of peripheral glucose utilization and hepatic glucose production, mainly by insulin. In this study, we found by utilizing a combined parallel chromatography mass profiling approach that lysophosphatidylcholine (LPC) regulates glucose levels. LPC was found to stimulate glucose uptake in 3T3-L1 adipocytes dose- and time-dependently, and this activity was found to be sensitive to variations in acyl chain lengths and to polar head group types in LPC. Treatment with LPC resulted in a significant increase in the level of GLUT4 at the plasma membranes of 3T3-L1 adipocytes. Moreover, LPC did not affect IRS-1 and AKT2 phosphorylations, and LPC-induced glucose uptake was not influenced by pretreatment with the PI 3-kinase inhibitor LY294002. However, glucose uptake stimulation by LPC was abrogated both by rottlerin (a protein kinase Cdelta inhibitor) and by the adenoviral expression of dominant negative protein kinase Cdelta. In line with its determined cellular functions, LPC was found to lower blood glucose levels in normal mice. Furthermore, LPC improved blood glucose levels in mouse models of type 1 and 2 diabetes. These results suggest that an understanding of the mode of action of LPC may provide a new perspective of glucose homeostasis.

Direct observation of interfacial C60 cluster formation in polystyrene-C60 nanocomposite films.

Large interfacial C(60) clusters were directly imaged at the supporting film-substrate interface in physically detached polystyrene-C(60) nanocomposite films by atomic force microscopy, confirming the stabilizing mechanism previously hypothesized for thin polymer films. Additionally, we found that the C(60) additive influences basic thermodynamic film properties such as the interfacial energy and the film thermal expansion coefficient.

Ligand profiling and identification technology for searching bioactive ligands.

We introduce a new methodology named ligand profiling and identification for effective discovery of bioactive ligands such as peptide hormones. This technology was developed from a new concept of parallel column chromatography and active fraction profiling by nano-LC MS. Traditional methods use sequential column chromatography, and thus are inevitably limited by the low abundance of the peptide of interest and by a low yield due to the many column steps. Using this new technology, insulin was successfully identified and diarginylinsulin, a minor intermediate form of insulin, was unexpectedly also identified simultaneously from 100 mg of porcine pancreatic tissue. This integrative technology could be used to search for various low-abundance peptides (or bioactive molecules) rapidly and simultaneously, by applying this to the later stages of traditional sequential purification.

Specular X-ray reflectivity and small angle neutron scattering for structure determination of ordered mesoporous dielectric films.

Specular X-ray reflectivity (SXR) and small-angle neutron scattering (SANS) are used to characterize the structure of a thin film containing cylindrical mesopores. The 3-D structure of the mesoporous film was determined from SANS measurements taken at multiple rotation angles between the incident beam and the film. The film was found to be composed of a randomly packed core and surface layers within which the hollow cylinders were regularly packed and oriented along the surface. The packing of the cylindrical mesopores was not hexagonal but rather rectangular with a conical angle of 55.7 degrees instead of 60 degrees expected for hexagonal packing. The extent of the planar orientation of the cylindrical mesopores within the surface layers was estimated from the width of the Bragg reflection in the SXR result to be about 25 repeating layers at both interfaces. This was further confirmed from cross-section transmission electron microscopy (TEM) results. The SXR results of this film exhibit an anomalous decrease in reflected intensity after each Bragg reflection. This anomaly in SXR can be modeled in a Parratt formulism using a depth profile composed of two characteristic lengths, the repeating distance among layers and the curvature of the density profile of each layer.

Characterization of pore structure in a nanoporous low-dielectric-constant thin film by neutron porosimetry and X-ray porosimetry.

A small-angle neutron scattering (SANS) porosimetry technique is presented for characterization of pore structure in nanoporous thin films. The technique is applied to characterize a spin-on organosilicate low dielectric constant (low-k) material with a random pore structure. Porosimetry experiments are conducted using a "contrast match" solvent (a mixture of toluene-d8 and toluene-h8) having the same neutron scattering length density as that of the nanoporous film matrix. The film is exposed to contrast match toluene vapor in a carrier gas (air), and pores fill with liquid by capillary condensation. The partial pressure of the solvent vapor is increased stepwise from 0 (pure air) to P0 (saturated solvent vapor) and then decreased stepwise to 0 (pure air). As the solvent partial pressure increases, pores fill with liquid solvent progressively from smallest to largest. SANS measurements quantify the average size of the empty pores (those not filled with contrast match solvent). Analogous porosimetry experiments using specular X-ray reflectivity (SXR) quantify the volume fraction of solvent adsorbed at each step. Combining SXR and SANS data yields information about the pore size distribution and illustrates the size dependence of the filling process. For comparison, the pore size distribution is also calculated by application of the classical Kelvin equation to the SXR data.

Moisture absorption and absorption kinetics in polyelectrolyte films: influence of film thickness.

Specular X-ray reflectivity (XR) and quartz crystal microbalance (QCM) measurements were used to determine the absorption of water into thin poly(4-ammonium styrenesulfonic acid) films from saturated vapor at 25 degrees C. The effect of film thickness on the absorption kinetics and overall absorption was investigated in the range of thickness from (3 to 200) nm. The equilibrium swelling of all the films irrespective of film thickness was (0.57+/-0.03) volume fraction. Although the equilibrium absorption is independent ofthickness, the absorption rate substantially decreases for film thickness < 100 nm. For the thinnest film (3 nm), there is a 5 orders of magnitude decrease in the diffusion coefficient for water.