Inferring epidemiological parameters from phylogenetic information for the HIV-1 epidemic among MSM

The HIV-1 epidemic in Europe is primarily sustained by a dynamic topology of sexual interactions among MSM who have individual immune systems and behavior. This epidemiological process shapes the phylogeny of the virus population. Both fields of epidemic modeling and phylogenetics have a long history, however it remains difficult to use phylogenetic data to infer epidemiological parameters such as the structure of the sexual network and the per-act infectiousness. This is because phylogenetic data is necessarily incomplete and ambiguous. Here we show that the cluster-size distribution indeed contains information about epidemiological parameters using detailed numberical experiments. We simulate the HIV epidemic among MSM many times using the Monte Carlo method with all parameter values and their ranges taken from literature. For each simulation and the corresponding set of parameter values we calculate the likelihood of reproducing an observed cluster-size distribution. The result is an estimated likelihood distribution of all parameters from the phylogenetic data, in particular the structure of the sexual network, the per-act infectiousness, and the risk behavior reduction upon diagnosis. These likelihood distributions encode the knowledge provided by the observed cluster-size distrbution, which we quantify using information theory. Our work suggests that the growing body of genetic data of patients can be exploited to understand the underlying epidemiological process.     

Detection of autocatalytic decomposition behavior of energetic materials using APTAC

Characterization of autocatalytic decomposition reactions is important for the safe handling and storage of energetic materials. Isothermal differential scanning calorimetry (DSC) has been widely used to detect autocatalytic decomposition of energetic materials. However, isothermal DSC tests are time consuming and the choice of experimental temperature is crucial. This paper shows that an automatic pressure tracking calorimeter (APTAC) can be a reliable and efficient screening tool for the identification of autocatalytic decomposition behavior of energetic materials. Hydroxylamine nitrate (HAN) is an important member of the hydroxylamine family. High concentrations of HAN are used as liquid propellants, and low concentrations of HAN are used primarily in the nuclear industry for decontamination of equipment. Because of its instability and autocatalytic decomposition behavior, HAN has been involved in several incidents.     

Loop grafting of Bacillus subtilis lipase A: inversion of enantioselectivity

Lipases are successfully applied in enantioselective biocatalysis. Most lipases contain a lid domain controlling access to the active site, but Bacillus subtilis Lipase A (LipA) is a notable exception: its active site is solvent exposed. To improve the enantioselectivity of LipA in the kinetic resolution of 1,2-O-isopropylidene-sn-glycerol (IPG) esters, we replaced a loop near the active-site entrance by longer loops originating from Fusarium solani cutinase and Penicillium purpurogenum acetylxylan esterase, thereby aiming to increase the interaction surface for the substrate. The resulting loop hybrids showed enantioselectivities inverted toward the desired enantiomer of IPG. The acetylxylan esterase-derived variant showed an inversion in enantiomeric excess (ee) from -12.9% to +6.0%, whereas the cutinase-derived variant was improved to an ee of +26.5%. The enantioselectivity of the cutinase-derived variant was further improved by directed evolution to an ee of +57.4%.     

Ultrafast magneto-optics in nickel: magnetism or optics?

Several magnetic and optical processes contribute to the magneto-optical response of nickel thin films after excitation by a femtosecond laser pulse. We achieved a first complete identification by explicitly measuring the time-resolved Kerr ellipticity and rotation, as well as its temperature and magnetic field dependence in epitaxially grown (111) and (001) oriented Cu/Ni/Cu wedges. The first hundreds of femtoseconds the response is dominated by state filling effects. The true demagnetization takes approximately 0.5-1 ps. At the longer (sub-ns) time scales the spins are found to precess in their anisotropy field. Simple and transparent models are introduced to substantiate our interpretation.     

A validated gas chromatographic method for the evaluation of enzymatic enantioselectivity in kinetic resolution applications

An enantioselective gas chromatography (GC) method has been developed and validated for determination of the enantiomers of citronellol in kinetic resolution experiments. S-(-)-beta-Citronellol is a precursor of rose oxide. After solid-phase extraction (SPE) with ethyl acetate, the enantiomers of R-(+)-beta-citronellol and S-(-)-beta-citronellol and their corresponding acetate- and butyrate esters were separated through enantioselective GC respectively. The method was validated and found to be reproducible, specific, accurate, and precise. Analyte recoveries and detection limits were also determined. The applicability of this method was shown in a kinetic resolution experiment using lipase A of Bacillus subtilis.