Investigation of the cell-wall loosening protein expansin as a possible additive in the enzymatic saccharification of lignocellulosic biomass

Applied Biochemistry and Biotechnology -     

Rapid identification of Candida albicans in blood by combined capillary electrophoresis and fluorescence in situ hybridization

A CE method based on whole‐cell molecular labeling via fluorescence in situ hybridization was developed for the detection of Candida albicans in whole blood. Removal of potentially interfering red blood cells (RBC) with a simple hypotonic/detergent lysis step enabled us to detect and quantitate contaminating C. albicans cells at concentrations that were orders of magnitude lower than background RBC counts (∼7.0×10⁹ RBC/mL). In the presence of the lysed blood matrix, yeast cells aggregated without the use of a blocking plug to stack the cells. Short (15 min) hybridizations yielded bright Candida‐specific fluorescence in situ hybridization signals, enabling us to detect as few as a single injected cell. The peak area response of the stacked Candida cells showed a strong linear correlation with cell concentrations determined by plate counts, up to ∼10⁷ CFU/mL (or ∼1×10⁴ injected cells). This rapid and quantitative method for detecting Candida in blood may have advantageous applications in both human and veterinary diagnostics.     

Properties of the He ground state from He neutron knockout

The unbound nucleus ⁷He, produced in neutron-knockout reactions with a 240 MeV/u ⁸He beam in a liquid-hydrogen target, has been studied in an experiment at the ALADIN-LAND setup at GSI. From an R-matrix analysis the resonance parameters for ⁷He as well as the spectroscopic factor for the ⁶He(0⁺) + n configuration in its ground-state have been obtained. The spectroscopic factor is 0.61 confirming that ⁷He is not a pure single-particle state. An analysis of ⁵He data from neutron-knockout reactions of ⁶He in a carbon target reveals the presence of an s  -wave component at low energies in the α+n$\alpha +\mathrm{n}$ relative energy spectrum.     

Computationally efficient implementation of combustion chemistry in parallel PDF calculations

In parallel calculations of combustion processes with realistic chemistry, the serial in situ adaptive tabulation (ISAT) algorithm [S.B. Pope, Computationally efficient implementation of combustion chemistry using in situ adaptive tabulation, Combustion Theory and Modelling, 1 (1997) 41–63; L. Lu, S.B. Pope, An improved algorithm for in situ   adaptive tabulation, Journal of Computational Physics 228 (2009) 361–386] substantially speeds up the chemistry calculations on each processor. To improve the parallel efficiency of large ensembles of such calculations in parallel computations, in this work, the ISAT algorithm is extended to the multi-processor environment, with the aim of minimizing the wall clock time required for the whole ensemble. Parallel ISAT strategies are developed by combining the existing serial ISAT algorithm with different distribution strategies, namely purely local processing (PLP), uniformly random distribution (URAN), and preferential distribution (PREF). The distribution strategies enable the queued load redistribution of chemistry calculations among processors using message passing. They are implemented in the software x2f_mpi$x2f\_\mathit{mpi}$, which is a Fortran 95 library for facilitating many parallel evaluations of a general vector function. The relative performance of the parallel ISAT strategies is investigated in different computational regimes via the PDF calculations of multiple partially stirred reactors burning methane/air mixtures. The results show that the performance of ISAT with a fixed distribution strategy strongly depends on certain computational regimes, based on how much memory is available and how much overlap exists between tabulated information on different processors. No one fixed strategy consistently achieves good performance in all the regimes. Therefore, an adaptive distribution strategy, which blends PLP, URAN and PREF, is devised and implemented. It yields consistently good performance in all regimes. In the adaptive parallel ISAT strategy, the type and extent of redistribution is determined “on the fly” based on the prediction of future simulation time. Compared to the PLP/ISAT strategy where chemistry calculations are essentially serial, a speed-up factor of up to 30 is achieved. The study also demonstrates that the adaptive strategy has acceptable parallel scalability.     

Systems biology of antibiotic production by microorganisms

The synthesis of secondary metabolites by microorganisms, specifically antibiotics, is of great scientific and economic importance. The onset (control and regulation) of secondary metabolite formation has and still is intriguing scientists both in industry and academia. Despite many studies, there is little known about the molecular mechanisms underlying the regulation of secondary metabolism. With the recent developments in genomics and further development of advanced post-genomic techniques, it will be possible to apply a more holistic analysis to the regulation of antibiotic production in microorganisms. Here we review current knowledge about the control and regulation of secondary metabolites, with a focus on antibiotics. We will also review developments in the genomics of antibiotic-producing microorganisms, and discuss the use of systems biology for gaining a better understanding of the networks involved in regulation of antibiotic production.     

Effective signal-to-noise ratio improvement by parametric image amplification

We show experimentally that parametric optical preamplification greatly improves the signal-to-noise ratio of an image if the detector has a poor quantum efficiency and/or a great level of readout noise. Results are fully consistent with the theory of quantum-noise-limited amplification.     

The use of cationic surfactants and ionic liquids in the detection of microbial contamination by capillary electrophoresis

A rapid test of whether a laboratory sample contains any microorganisms is important and necessary for many areas of science and technology. Currently, most of the standard procedures for the detection of aerobic bacteria, anaerobic bacteria and fungi, require the preparation of microbial cultures in respective growth media, which are dramatically slow. Different approaches providing fast analysis such as CE are becoming more desired. To compensate for the natural electrophoretic heterogeneity of microbes, various buffer additives were examined to stack all bacteria and fungi in a sample plug into a single peak. This peak was removed from the molecular contaminants in the sample to prevent false positives. Both cationic surfactants and ionic liquids (IL) were investigated as run buffer additives and they are both widely applicable to different species of bacteria and fungi. Given that high concentrations of surfactants can potentially lyse cells, dicationic IL offer attractive auxiliary buffer additives for use in CE-based sterility tests. The analysis can be completed in 10 min, thus providing a great advantage over traditional direct inoculation methods that require several weeks to complete.