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Draft whole-genome sequence of the fluorene-degrading sphingobium sp. strain LB126, isolated from polycyclic aromatic hydrocarbon-contaminated soil
No full textWe report here the draft whole-genome sequence of a fluorene-degrading bacterium, Sphingobium sp. strain LB126. The genes involved in the upper biodegradation pathway of fluorene are located on a plasmid, and the lower pathway that generates tricarboxylic acid cycle intermediates is initiated by the meta-cleavage of protocatechuic acid that is chromosomally encoded.Peer reviewed: YesNRC publication: Ye
Dynamics at conical intersections
No full textThe nonadiabatic coupling of electronic and vibrational degrees of freedom is the defining feature of electronically excited states of polyatomic molecules. Once considered a theoretical curiosity, conical intersections (CIs) are now generally accepted as being the dominant source of coupled charge and vibrational energy flow in molecular excited states. Passage through CIs leads to the conversion of electronic to vibrational energy, which drives the ensuing photochemistry, isomerization being a canonical example. It has often been remarked that the CI may be thought of as a transition state in the excited state. As such, we expect that both the direction and the velocity of approach to the CI will matter. We explore this suggestion by looking for dynamical aspects of passage through CIs and for analogies with well-known concepts from ground-state reaction dynamics. Great progress has been made in the development of both experimental techniques and ab initio dynamics simulations, to a degree that direct comparisons may now be made. Here we compare time-resolved photoelectron spectroscopy results with on-the-fly ab initio multiple spawning calculations of the experimental observables, thereby validating each. We adopt a phenomenological approach and specifically concentrate on the excited-state dynamics of the C=C bond in unsaturated hydrocarbons. In particular, we make use of selective chemical substitution (such as replacing an H atom by a methyl group) so as to alter the inertia of certain vibrations relative to others, thus systematically varying (mass-weighted) directions and velocities of approach to a CI. Chemical substituents, however, may affect both the nuclear and electronic components of the total wave function. The former, which we call an inertial effect, influences the direction and velocity of approach. The latter, which we call a potential effect, modifies the electronic structure and therefore the energetic location and topography of the potential energy surfaces involved. Using a series of examples, we discuss both types of effects. We argue that there is a need for dynamical pictures and simple models of nonadiabatic dynamics at CIs and hope that the phenomenology presented here will help inspire such developments.Peer reviewed: YesNRC publication: Ye
Dynamics of paralytic shellfish toxins and their metabolites during timecourse exposure of scallops Chlamys farreri and mussels Mytilus galloprovincialis to Alexandrium pacificum
No full textNew C-11 hydroxyl metabolites of paralytic shellfish toxins (PSTs) have been reported in shellfish. To gain further information on these metabolites, as well as the potential for formation of phase-II metabolites and acyl esters of PSTs, bivalves were fed with the PSTs-producing dinoflagellate Alexandrium pacificum (strain ATHK). Through independent experiments, scallops (Chlamys farreri) were fed for 9\u202fdays and mussels (Mytilus galloprovincialis) for 5\u202fdays plus an additional 5\u202fdays of depuration, with representative samples taken throughout. Several common PSTs (C1-4, GTX1-6 and NEO) and metabolites including M1, M3, M5, M7, M9, M2 and M8 were detected in the hepatopancreas of scallops during toxin accumulation and in the hepatopancreas of mussels during both toxin accumulation and elimination periods. The relative molar ratio of metabolites to precursor molecules was used to estimate relative metabolic conversion rates. Conversion rates of C1/2 and GTX2/3 were higher than those of C3/4 and GTX1/4, in scallops and mussels. The first metabolites observed in both bivalve species investigated were M1/3, which are formed from C1/2. However, the conversion of GTX2/3 to M2 was more complete than other biotransformation reactions in both mussels and scallops. In general, metabolic conversion of PSTs was observed after a shorter time and to a greater extent in mussels than in scallops in the exposure period. No acyl esters or conjugation products of PSTs with glucuronic acid, glutathione, cysteine and taurine were detected by liquid chromatography with high resolution tandem mass spectrometry in the samples investigated. Additionally, only GTX1/4 and GTX2/3 were detected in the kidney of scallops, which demonstrates that PSTs are mainly metabolized through the hepatic metabolism pathway in bivalves. This work improves the understanding of PST metabolism during toxin accumulation and depuration in commercially harvested shellfish.Peer reviewed: YesNRC publication: Ye
ATP triggers a robust intracellular [Ca2+]-mediated signalling pathway in human synovial fibroblasts
No full textIn human articular joints, synovial fibroblasts (HSFs) have essential physiological functions that include synthesis and secretion of components of the extracellular matrix and essential articular joint lubricants, as well as release of paracrine substances such as ATP. Although the molecular and cellular processes that lead to a rheumatoid arthritis (RA) phenotype are not fully understood, HSF cells exhibit significant changes during this disease progression. The effects of ATP on HSFs were studied by monitoring changes in intracellular Ca2+ ([Ca2+]i), and measuring electrophysiological properties. ATP application to HSF cell populations that had been enzymatically released from 2\u2010D cell culture revealed that ATP (10\u2013100 \u3bcm), or its analogues UTP or ADP, consistently produced a large transient increase in [Ca2+]i. These changes (i) were initiated by activation of the P2Y purinergic receptor family, (ii) required Gq\u2010mediated signal transduction, (iii) did not involve a transmembrane Ca2+ influx, but instead (iv) arose almost entirely from activation of endoplasmic reticulum (ER)\u2010localized inositol 1,4,5\u2010trisphosphate (IP3) receptors that triggered Ca2+ release from the ER. Corresponding single cell electrophysiological studies revealed that these ATP effects (i) were insensitive to [Ca2+]o removal, (ii) involved an IP3\u2010mediated intracellular Ca2+ release process, and (iii) strongly turned on Ca2+\u2010activated K+ current(s) that significantly hyperpolarized these cells. Application of histamine produced very similar effects in these HSF cells. Since ATP is a known paracrine agonist and histamine is released early in the inflammatory response, these findings may contribute to identification of early steps/defects in the initiation and progression of RA.Peer reviewed: YesNRC publication: Ye
Effects of stem-injected gibberellins and 6-benzylaminopurine on phytohormone profiles and cone yield in two lodgepole pine genotypes
No full textEffects of exogenously applied gibberellins (GAs) and 6-benzylaminopurine (BA) on profiles of phytohormones and some of their metabolites relative to controls in long-shoot buds of lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) were analyzed during cone bud initiation and differentiation. Differential responses in phytohormones and in cone yield were observed in ramets of the two tested genotypes (478 and 276) to stem-injected mixtures of GA4 and GA7 (GA4/7) and /or BA. Injected GA4/7 affected bud concentrations of GA4 and GA7. Injected PGRs, with the exception of BA injection, decreased concentrations of abscisic acid (ABA) and ABA glucose-ester at week 5 and/or week 7. Internal concentrations of trans-zeatin riboside (t-ZR) increased in response to all treatments at week 3 in genotype 276. In genotype 478, t-ZR only increased with treatments of BA or GA4/7 plus BA. Dihydrozeatin riboside concentrations increased in response to GA4/7 plus BA treatment at week 7 in genotype 276. Concentrations of isopentenyl adenosine declined with treatments of GA4/7 and GA4/7 plus BA in genotype 276 at week 5. In genotype 478, a similar decrease was caused by GA4/7 plus BA treatment. For both genotypes, the highest ratio of zeatin-type cytokinins to isopentenyl-type cytokinins occurred at weeks 5 and 7 after injection with GA4/7 plus BA. Stem-injection of GA4/7, especially in combination with BA, increased female cone yields significantly in genotype 276, but not in genotype 478.Peer reviewed: YesNRC publication: Ye
Full-length glycosylated gag of murine leukemia virus can associate with the viral envelope as a type I integral membrane protein
No full textThe glycosylated Gag protein (gPr80) of murine leukemia viruses (MLVs) has been shown to exhibit multiple roles in facilitating retrovirus release, infection, and resistance to host-encoded retroviral restriction factors, such as APOBEC3, SERINC3, and SERINC5. One way in which gPr80 helps MLVs to escape host innate immune restriction is by increasing capsid stability, a feature that protects viral replication intermediates from being detected by cytosolic DNA sensors. gPr80 also increases the resistance of MLVs to deamination and restriction by mouse APOBEC3 (mA3). How the gPr80 accessory protein, with its three N-linked glycosylation sites, contributes to these resistance mechanisms is still not fully understood. Here we further characterized the function of gPr80 and, more specifically, revealed that the asparagines targeted for glycosylation in gPr80 also contribute to capsid stability through their parallel involvement in the Pr65 Gag structural polyprotein. In fact, we demonstrate that sensitivity to deamination by the mA3 and human A3 proteins is directly linked to capsid stability. We also show that full-length gPr80 is detected in purified viruses. However, our results suggest that gPr80 is inserted in the NexoCcyto orientation of a type I integral membrane protein. Additionally, our experiments have revealed the existence of a large population of Env-deficient virus-like particles (VLPs) harboring gPr80 inserted in the opposite (NcytoCexo) polarity, which is typical of type II integral membrane proteins. Overall this study provides new insight into the complex nature of the MLV gPr80 accessory protein.Peer reviewed: YesNRC publication: Ye
Gene transfer of ZMapp antibodies mediated by recombinant adeno-associatedvVirus protects against Ebola infections
No full textVectored delivery of the ZMapp antibody cocktail (c2G4, c4G7, and c13C6) by using recombinant adeno-associated viruses (rAAVs) could be useful for preventive immunization against Ebola virus infections because rAAVs can generate long-term antibody expression. Three rAAVs (serotype 9) encoding chimeric ZMapp antibodies were produced by triple-plasmid transfection up to 10\u2009L-scale in WAVE bioreactors using HEK293 cells grown in suspension/serum-free conditions. Efficacy of AAV-c2G4 via intravenous (i.v.), intramuscular (i.m.), and intranasal (i.n.) routes of administration was evaluated in mice with two different doses of 2.7\u2009
7\u20091010 and 13.0\u2009
7\u20091010 vector genomes (vg). The best protective efficacies after Ebola challenge were obtained with the i.v. and i.m. routes. Serum concentrations of ZMapp antibodies positively correlated with survivability. Efficacy of the rAAV-ZMapp cocktail was then evaluated at a higher dose of 30.0\u2009
7\u20091010 vg. It conferred a more robust protection (90% i.v. and 60% i.m.) than rAAV-c4G7 (30%) and rAAV-c13C6 (70%), both administered separately at the same dose. Delivery of rAAV-c2G4 alone achieved up to 100% protection (100% i.v. and 90% i.m.) at the same dose. In conclusion, the preventive treatment was effective in mice. However, no advantage was observed for using the rAAV-ZMapp cocktail in comparison to the utilization of the single rAAV-c2G4.Peer reviewed: YesNRC publication: Ye
High performance InAs/InP quantum dot 34462-GHz C-band coherent comb laser module
No full textWe have developed an InAs/InP quantum dot (QD) C-band coherent comb laser (CCL) module with actively stabilized absolute wavelength and power, and channel spacing of 34.462 GHz with \ub1 100 ppm accuracy. The total output power is up to 46 mW. The integrated average relative intensity noise (RIN) values of the lasing spectrum and a filtered single channel at 1540.19 nm were 12165.6 dB/Hz and 12130.3 dB/Hz respectively in the frequency range from 10 MHz to 10 GHz. The optical linewidth of the 45 filtered individual channels between 1531.77 nm to 1543.77 nm ranged from 850 kHz to 2.16 MHz. We have also analyzed the noise behaviors of each individual channel.Peer reviewed: YesNRC publication: Ye
High-temperature and low-threshold interband cascade lasers at wavelengths longer than 6\u2009\u2009\u3bcm
No full textInAs-based interband cascade (IC) lasers with improved optical confinement have achieved high-temperature operation with a threshold current density as low as 333 A 15cm2 at 300 K for emission at 6003 nm. The threshold current density is the lowest ever reported among semiconductor midinfrared lasers at similar wavelengths. These InAs-based IC devices lased in pulsed mode at temperatures up to 357 K near 6.28 \u3bcm. A narrow-ridge device was able to operate in continuous-wave mode at temperatures up to 293 K at 6.01 \u3bcm.Peer reviewed: YesNRC publication: Ye
Infrared spectra of C2H4 dimer and trimer
No full textSpectra of ethylene dimers and trimers are studied in the \u3bd11 and (for the dimer) \u3bd9 fundamental band regions of C2H4 ( 482990 and 3100\u202fcm 121) using a tunable optical parametric oscillator source to probe a pulsed supersonic slit jet expansion. The deuterated trimer has been observed previously, but this represents the first rotationally resolved spectrum of (C2H4)3. The results support the previously determined cross-shaped (D2d) dimer and barrel-shaped (C3h or C3) trimer structures. However, the dimer spectrum in the \u3bd9 fundamental region of C2H4 is apparently very perturbed and a previous rotational analysis is not well verified.Peer reviewed: YesNRC publication: Ye