Bench-top X-ray microtomography complemented with spatially localized X-ray scattering experiments

This article describes a novel experimental setup that combines X-ray microtomography (XMT) scans with in situ X-ray scattering experiments in a laboratory setting. Combining these two methods allows the characterization of both the micrometre-scale morphology and the crystallographic properties of the sample without removing it from the setup. Precise control of the position of the sample allows an accurate choice of the scattering beam path through the sample and facilitates the performance of X-ray scattering experiments on submillimetre-sized samples. With the present setup, a voxel size of less than 0.5 mm is achievable in the XMT images, and scattering experiments can be carried out with a beam size of approximately 200 200 mm. The potential of this setup is illustrated with the analysis of micrometeorite crystal structure and diffraction tomographic imaging of a silver behenate phantom as example applications.Peer reviewe

Johann-type laboratory-scale x-ray absorption spectrometer with versatile detection modes

We present a low-cost laboratory X-ray absorption spectrometer that uses a conventional X-ray tube source and bent Johann-type crystal monochromators. The instrument is designed for X-ray absorption spectroscopy studies in the 4-20 keV range which covers most K edges of 3d transition metals and L edges of 5d transition metals and actinides. The energy resolution is typically in the range of 1-5 eV at 10 keV depending on the crystal analyser and the Bragg angle. Measurements can be performed in transmission, fluorescence, and imaging modes. Due to its simple and modular design, the spectrometer can be modified to accommodate additional equipment and complex sample environments required for in situ studies. A showcase of various applications is presented. Published under license by AIP Publishing.Peer reviewe

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

Peer reviewe

Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction

Background: Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis. Results: A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model. Conclusions: The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1on-strate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes.Peer reviewe

Evolutionary Conservation of Orthoretroviral Long Terminal Repeats (LTRs) and ab initio Detection of Single LTRs in Genomic Data

Background: Retroviral LTRs, paired or single, influence the transcription of both retroviral and non-retroviral genomic sequences. Vertebrate genomes contain many thousand endogenous retroviruses (ERVs) and their LTRs. Single LTRs are difficult to detect from genomic sequences without recourse to repetitiveness or presence in a proviral structure. Understanding of LTR structure increases understanding of LTR function, and of functional genomics. Here we develop models of orthoretroviral LTRs useful for detection in genomes and for structural analysis. Principal Findings: Although mutated, ERV LTRs are more numerous and diverse than exogenous retroviral (XRV) LTRs. Hidden Markov models (HMMs), and alignments based on them, were created for HML- (human MMTV-like), general-beta-, gamma- and lentiretroviruslike LTRs, plus a general-vertebrate LTR model. Training sets were XRV LTRs and RepBase LTR consensuses. The HML HMM was most sensitive and detected 87% of the HML LTRs in human chromosome 19 at 96% specificity. By combining all HMMs with a low cutoff, for screening, 71% of all LTRs found by RepeatMasker in chromosome 19 were found. HMM consensus sequences had a conserved modular LTR structure. Target site duplications (TG-CA), TATA (occasionally absent), an AATAAA box and a T-rich region were prominent features. Most of the conservation was located in, or adjacent to, R and U5, with evidence for stem loops. Several of the long HML LTRs contained long ORFs inserted after the second A rich module. HMM consensus alignment allowed comparison of functional features like transcriptional start sites (sense and antisense) between XRVs and ERVs. Conclusion: The modular conserved and redundant orthoretroviral LTR structure with three A-rich regions is reminiscent of structurally relaxed Giardia promoters. The five HMMs provided a novel broad range, repeat-independent, ab initio LTR detection, with prospects for greater generalisation, and insight into LTR structure, which may aid development of LTR-targeted pharmaceuticals.Peer reviewe

Perustulokokeilun hyvinvointivaikutuksia

Non peer reviewe