The Modern Epidemic of Syphilis Ghanem, Khalil G; Ram, Sanjay; Rice, Peter A
The New England journal of medicine,
02/2020, Letnik:
382, Številka:
9
Journal Article
The systematic improvement of Fe–N–C materials for fuel cell applications has proven challenging, due in part to an incomplete atomistic understanding of the oxygen reduction reaction (ORR) under ...electrochemical conditions. Herein, a multilevel computational approach, which combines ab initio molecular dynamics simulations and constant potential density functional theory calculations, is used to assess proton-coupled electron transfer (PCET) processes and adsorption thermodynamics of key ORR intermediates. These calculations indicate that the potential-limiting step for ORR on Fe–N–C materials is the formation of the FeIII–OOH intermediate. They also show that an active site model with a water molecule axially ligated to the iron center throughout the catalytic cycle produces results that are consistent with the experimental measurements. In particular, reliable prediction of the ORR onset potential and the Fe(III/II) redox potential associated with the conversion of FeIII–OH to FeII and desorbed H2O requires an axial H2O co-adsorbed to the iron center. The observation of a five-coordinate rather than four-coordinate active site has significant implications for the thermodynamics and mechanism of ORR. These findings highlight the importance of solvent–substrate interactions and surface charge effects for understanding the PCET reaction mechanisms and transition-metal redox couples under realistic electrochemical conditions.
Gonorrhea, an obligate human infection, is on the rise worldwide and gonococcal strains resistant to many antibiotics are emerging. Appropriate antimicrobial treatment and prevention, including ...effective vaccines, are urgently needed. To guide investigation, an experimental model of genital tract infection has been developed in female mice to study mechanisms by which
Neisseria gonorrhoeae
evades host-derived antimicrobial factors and to identify protective and immunosuppressive pathways. Refinements of the animal model have also improved its use as a surrogate host of human infection and accelerated the testing of novel therapeutic and prophylactic compounds against gonococcal infection. Reviewed herein are the (
a
) history of antibiotic usage and resistance against gonorrhea and the consequences of resistance mechanisms that may increase gonococcal fitness and therefore the potential for spread, (
b
) use of gonococcal infection in the animal model system to study mechanisms of pathogenesis and host defenses, and (
c
) current status of vaccine development.
FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite lacking any formal definition to date, and ...existing in at least three incompatible variants. This article defines the FASTQ format, covering the original Sanger standard, the Solexa/Illumina variants and conversion between them, based on publicly available information such as the MAQ documentation and conventions recently agreed by the Open Bioinformatics Foundation projects Biopython, BioPerl, BioRuby, BioJava and EMBOSS. Being an open access publication, it is hoped that this description, with the example files provided as Supplementary Data, will serve in future as a reference for this important file format.
To date, the understanding of reactions at solid–liquid interfaces has proven challenging, mainly because of the inaccessible nature of such systems to current experimental techniques with atomic ...resolution. This has meant that many important features, including free energy barriers and the atomistic structure of intermediates, remain unknown. To tackle these issues, we construct and utilize a high-dimensional neural network (HDNN) potential for the simulation of hydrogen evolution at the HCl(aq)/Pt(111) interface, taking into consideration the influence of adsorbate–adsorbate, adsorbate–solvent interactions, and ion solvation explicitly. Long time scale MD simulations reveal coadsorbed Had/H2Oad on the surface. The free energy profiles for the Tafel and Heyrovsky type hydrogen coupling are extracted using umbrella sampling. It is found that the preferential mechanism can change depending on the surface coverage, highlighting the dual mechanistic nature for HER on Pt(111). Our work demonstrates the importance of controlling the solvent–substrate interactions in developing catalysts beyond Pt.
Carbon sorbent materials have shown great promise for solid‐state hydrogen (H2) storage. Modification of these materials with nitrogen (N) dopants has been undertaken to develop materials that can ...store H2 at ambient temperatures. In this work density functional theory (DFT) calculations are used to systematically probe the influence of curvature on the stability and activity of undoped and N‐doped carbon materials toward H binding. Specifically, four models of carbon materials are used: graphene, 5,5 carbon nanotube, 5,5 D5d‐C120, and C60, to extract and correlate the thermodynamic properties of active sites with varying degrees of sp2 hybridization (curvature). From the calculations and analysis, it is found that graphitic N‐doping is thermodynamically favored on more pyramidal sites with increased curvature. In contrast, it is found that the hydrogen binding energy is weakly affected by curvature and is dominated by electronic effects induced by N‐doping. These findings highlight the importance of modulating the heteroatom doping configuration and the lattice topology when developing materials for H2 storage.
Using four models of carbon materials: graphene, 5,5 carbon nanotube, 5,5 D5d‐C120, and C60, the thermodynamic properties of active sites with varying degrees of curvature and graphitic N‐doping are correlated. The DFT calculations show that graphitic N‐doping is thermodynamically favored with increased curvaturewhile the hydrogen binding energy is weakly affected by curvature and is dominated by N‐doping.
Multidrug-resistant Neisseria gonorrhoeae is a global health problem. Monoclonal antibody (mAb) 2C7 recognizes a gonococcal lipooligosaccharide epitope that is expressed by >95% of clinical isolates ...and hastens gonococcal vaginal clearance in mice. Chimeric mAb 2C7 (human immunoglobulin G1 IgG1) with an E430G Fc modification that enhances Fc:Fc interactions and hexamerization following surface-target binding and increases complement activation (HexaBody technology) showed significantly greater C1q engagement and C4 and C3 deposition compared to mAb 2C7 with wild-type Fc. Greater complement activation by 2C7-E430G Fc translated to increased bactericidal activity in vitro and, consequently, enhanced efficacy in mice, compared with "Fc-unmodified" chimeric 2C7. Gonococci bind the complement inhibitors factor H (FH) and C4b-binding protein (C4BP) in a human-specific manner, which dampens antibody (Ab)-mediated complement-dependent killing. The variant 2C7-E430G Fc overcame the barrier posed by these inhibitors in human FH/C4BP transgenic mice, for which a single 1 μg intravenous dose cleared established infection. Chlamydia frequently coexists with and exacerbates gonorrhea; 2C7-E430G Fc also proved effective against gonorrhea in gonorrhea/chlamydia-coinfected mice. Complement activation alone was necessary and sufficient for 2C7 function, evidenced by the fact that (1) "complement-inactive" Fc modifications that engaged Fc gamma receptor (FcγR) rendered 2C7 ineffective, nonetheless; (2) 2C7 was nonfunctional in C1q-/- mice, when C5 function was blocked, or in C9-/- mice; and (3) 2C7 remained effective in neutrophil-depleted mice and in mice treated with PMX205, a C5a receptor (C5aR1) inhibitor. We highlight the importance of complement activation for antigonococcal Ab function in the genital tract. Elucidating the correlates of protection against gonorrhea will inform the development of Ab-based gonococcal vaccines and immunotherapeutics.
Gonorrhea is a highly prevalent disease resulting in significant morbidity worldwide, with an estimated 106 cases reported annually. Neisseria gonorrhoeae, the causative agent of gonorrhea, colonizes ...and infects the human genital tract and often evades host immune mechanisms until successful antibiotic treatment is used. The alarming increase in antibiotic-resistant strains of N. gonorrhoeae, the often asymptomatic nature of this disease in women and the lack of a vaccine directed at crucial virulence determinants have prompted us to perform transcriptome analysis to understand gonococcal gene expression patterns during natural infection. We sequenced RNA extracted from cervico-vaginal lavage samples collected from women recently exposed to infected male partners and determined the complete N. gonorrhoeae transcriptome during infection of the lower genital tract in women. On average, 3.19% of total RNA isolated from female samples aligned to the N. gonorrhoeae NCCP11945 genome and 1750 gonococcal ORFs (65% of all protein-coding genes) were transcribed. High expression in vivo was observed in genes encoding antimicrobial efflux pumps, iron response, phage production, pilin structure, outer membrane structures and hypothetical proteins. A parallel analysis was performed using the same strains grown in vitro in a chemically defined media (CDM). A total of 140 genes were increased in expression during natural infection compared to growth in CDM, and 165 genes were decreased in expression. Large differences were found in gene expression profiles under each condition, particularly with genes involved in DNA and RNA processing, iron, transposase, pilin and lipoproteins. We specifically interrogated genes encoding DNA binding regulators and iron-scavenging proteins, and identified increased expression of several iron-regulated genes, including tbpAB and fbpAB, during infection in women as compared to growth in vitro, suggesting that during infection of the genital tract in women, the gonococcus is exposed to an iron deplete environment. Collectively, we demonstrate that a large portion of the gonococcal genome is expressed and regulated during mucosal infection including genes involved in regulatory functions and iron scavenging.
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