Intramolecular vibronic dynamics in molecular solids: C60

Vibronic coupling in solid C60 has been investigated with a combination of resonant photoemission spectroscopy (RPES) and resonant inelastic x-ray scattering (RIXS). Excitation as a function of energy within the lowest unoccupied molecular orbital resonance yielded strong oscillations in intensity and dispersion in RPES, and a strong inelastic component in RIXS. Reconciling these two observations establishes that vibronic coupling in this core hole excitation leads to predominantly inelastic scattering and localization of the excited vibrations on the molecule on a femtosecond time scale. The coupling extends throughout the widths of the frontier valence bands.

Disordered systems on various time scales: a-Si3B3N7 and homogeneous sintering

Modeling of materials systems for long times commonly requires the use of separation of time scale methods. We discuss this general approach and present two example systems, a-Si3B3N7 and the generation of homogeneous sinters.Comment: 22 pages, 7 figure

A systems approach to model natural variation in reactive properties of bacterial ribosomes

<p>Abstract</p> <p>Background</p> <p>Natural variation in protein output from translation in bacteria and archaea may be an organism-specific property of the ribosome. This paper adopts a systems approach to model the protein output as a measure of specific ribosome reactive properties in a ribosome-mediated translation apparatus. We use the steady-state assumption to define a transition state complex for the ribosome, coupled with mRNA, tRNA, amino acids and reaction factors, as a subsystem that allows a focus on the completed translational output as a measure of specific properties of the ribosome.</p> <p>Results</p> <p>In analogy to the steady-state reaction of an enzyme complex, we propose a steady-state translation complex for mRNA from any gene, and derive a maximum specific translation activity, <it>T</it>_{<it>a</it>(max)}, as a property of the ribosomal reaction complex. <it>T</it>_{<it>a</it>(max)}has units of <it>a</it>-protein output per time per <it>a</it>-specific mRNA. A related property of the ribosome, <inline-formula><m:math name="1752-0509-2-62-i1" xmlns:m="http://www.w3.org/1998/Math/MathML"><m:semantics><m:mrow><m:msub><m:mover accent="true"><m:mi>T</m:mi><m:mo>˜</m:mo></m:mover><m:mrow><m:mi>a</m:mi><m:mo stretchy="false">(</m:mo><m:mi>max</m:mi><m:mo>⁡</m:mo><m:mo stretchy="false">)</m:mo></m:mrow></m:msub></m:mrow><m:annotation encoding="MathType-MTEF"> MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGafmivaqLbaGaadaWgaaWcbaGaemyyaeMaeiikaGIagiyBa0MaeiyyaeMaeiiEaGNaeiykaKcabeaaaaa@3464@</m:annotation></m:semantics></m:math></inline-formula>, has units of <it>a</it>-protein per time per total RNA with the relationship <inline-formula><m:math name="1752-0509-2-62-i1" xmlns:m="http://www.w3.org/1998/Math/MathML"><m:semantics><m:mrow><m:msub><m:mover accent="true"><m:mi>T</m:mi><m:mo>˜</m:mo></m:mover><m:mrow><m:mi>a</m:mi><m:mo stretchy="false">(</m:mo><m:mi>max</m:mi><m:mo>⁡</m:mo><m:mo stretchy="false">)</m:mo></m:mrow></m:msub></m:mrow><m:annotation encoding="MathType-MTEF"> MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGafmivaqLbaGaadaWgaaWcbaGaemyyaeMaeiikaGIagiyBa0MaeiyyaeMaeiiEaGNaeiykaKcabeaaaaa@3464@</m:annotation></m:semantics></m:math></inline-formula> = <it>ρ</it>_{<it>a </it>}<it>T</it>_{<it>a</it>(max)}, where <it>ρ</it>_{<it>a </it>}represents the fraction of total RNA committed to translation output of <it>P</it>_{<it>a </it>}from gene <it>a </it>message. <it>T</it>_{<it>a</it>(max)}as a ribosome property is analogous to <it>k</it>_catfor a purified enzyme, and <inline-formula><m:math name="1752-0509-2-62-i1" xmlns:m="http://www.w3.org/1998/Math/MathML"><m:semantics><m:mrow><m:msub><m:mover accent="true"><m:mi>T</m:mi><m:mo>˜</m:mo></m:mover><m:mrow><m:mi>a</m:mi><m:mo stretchy="false">(</m:mo><m:mi>max</m:mi><m:mo>⁡</m:mo><m:mo stretchy="false">)</m:mo></m:mrow></m:msub></m:mrow><m:annotation encoding="MathType-MTEF"> MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGafmivaqLbaGaadaWgaaWcbaGaemyyaeMaeiikaGIagiyBa0MaeiyyaeMaeiiEaGNaeiykaKcabeaaaaa@3464@</m:annotation></m:semantics></m:math></inline-formula> is analogous to enzyme specific activity in a crude extract.</p> <p>Conclusion</p> <p>Analogy to an enzyme reaction complex led us to a ribosome reaction model for measuring specific translation activity of a bacterial ribosome. We propose to use this model to design experimental tests of our hypothesis that specific translation activity is a ribosomal property that is subject to natural variation and natural selection much like <it>V</it>_maxand <it>K</it>_mfor any specific enzyme.</p

Multiplex PCR for detection of plasmid-mediated colistin resistance determinants, mcr-1, mcr-2, mcr-3, mcr-4 and mcr-5 for surveillance purposes

Background and aim: Plasmid-mediated colistin resistance mechanisms have been identified worldwide in the past years. A multiplex polymerase chain reaction (PCR) protocol for detection of all currently known transferable colistin resistance genes (mcr-1 to mcr-5, and variants) in Enterobacteriaceae was developed for surveillance or research purposes. Methods: We designed four new primer pairs to amplify mcr-1, mcr-2, mcr-3 and mcr-4 gene products and used the originally described primers for mcr-5 to obtain a stepwise separation of ca 200 bp between ampli-cons. The primer pairs and amplification conditions allow for single or multiple detection of all currently described mcr genes and their variants present in Enterobacteriaceae. The protocol was validated testing 49 European Escherichia coli and Salmonella isolates of animal origin. Results: Multiplex PCR results in bovine and porcine isolates from Spain, Germany, France and Italy showed full concordance with whole genome sequence data. The method was able to detect mcr-1, mcr-3 and mcr-4 as singletons or in different combinations as they were present in the test isolates. One new mcr-4 variant, mcr-4.3, was also identified. Conclusions: This method allows rapid identification of mcr-positive bacteria and overcomes the challenges of phenotypic detection of colistin resistance. The multiplex PCR should be particularly interesting in settings or laboratories with limited resources for performing genetic analysis as it provides information on the mechanism of colistin resistance without requiring genome sequencing. © 2018, European Centre for Disease Prevention and Control (ECDC). All rights reserved

Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM

The accuracy of ribosomal translation is achieved by an initial selection and a proofreading step, mediated by EF-Tu, which forms a ternary complex with aminoacyl(aa)-tRNA. To study the binding modes of different aa-tRNAs, we compared cryo-EM maps of the kirromycin-stalled ribosome bound with ternary complexes containing Phe-tRNAPhe, Trp-tRNATrp, or Leu-tRNALeuI. The three maps suggest a common binding manner of cognate aa-tRNAs in their specific binding with both the ribosome and EF-Tu. All three aa-tRNAs have the same ‘loaded spring' conformation with a kink and twist between the D-stem and anticodon stem. The three complexes are similarly integrated in an interaction network, extending from the anticodon loop through h44 and protein S12 to the EF-Tu-binding CCA end of aa-tRNA, proposed to signal cognate codon–anticodon interaction to the GTPase centre and tune the accuracy of aa-tRNA selection