Metabolomics methods for the synthetic biology of secondary metabolism

Many microbial secondary metabolites are of high biotechnological value for medicine, agriculture, and the food industry. Bacterial genome mining has revealed numerous novel secondary metabolite biosynthetic gene clusters, which encode the potential to synthesize a large diversity of compounds that have never been observed before. The stimulation or “awakening” of this cryptic microbial secondary metabolism has naturally attracted the attention of synthetic microbiologists, who exploit recent advances in DNA sequencing and synthesis to achieve unprecedented control over metabolic pathways. One of the indispensable tools in the synthetic biology toolbox is metabolomics, the global quantification of small biomolecules. This review illustrates the pivotal role of metabolomics for the synthetic microbiology of secondary metabolism, including its crucial role in novel compound discovery in microbes, the examination of side products of engineered metabolic pathways, as well as the identification of major bottlenecks for the overproduction of compounds of interest, especially in combination with metabolic modeling. We conclude by highlighting remaining challenges and recent technological advances that will drive metabolomics towards fulfilling its potential as a cornerstone technology of synthetic microbiology

Age-related impairment of mesenchymal progenitor cell function

In most mesenchymal tissues a subcompartment of multipotent progenitor cells is responsible for the maintenance and repair of the tissue following trauma. With increasing age, the ability of tissues to repair themselves is diminished, which may be due to reduced functional capacity of the progenitor cells. The purpose of this study was to investigate the effect of aging on rat mesenchymal progenitor cells. Mesenchymal progenitor cells were isolated from Wistar rats aged 3, 7, 12 and 56 weeks. Viability, capacity for differentiation and cellular aging were examined. Cells from the oldest group accumulated raised levels of oxidized proteins and lipids and showed decreased levels of antioxidative enzyme activity. This was reflected in decreased fibroblast colony-forming unit (CFU-f) numbers, increased levels of apoptosis and reduced proliferation and potential for differentiation. These data suggest that the reduced ability to maintain mesenchymal tissue homeostasis in aged mammals is not purely due to a decline in progenitor cells numbers but also to a loss of progenitor functionality due to the accumulation of oxidative damage, which may in turn be a causative factor in a number of age-related pathologies such as arthritis, tendinosis and osteoporosis. © 2006 The Authors Journal compilation © Blackwell Publishing Ltd/Anatomical Society of Great Britain and Ireland 2006

Study of Radiologic Technologists’ Perceptions of Picture Archiving and Communication System (PACS) Competence and Educational Issues in Western Australia

Although the implementation of picture archiving and communication system (PACS) could increase productivity of radiology departments, this depends on factors such as the PACS competence of radiologic technologists (RTs). The purpose of this study was to investigate the RTs’ perceptions of PACS competence and educational issues in Western Australia (WA). A hardcopy questionnaire was distributed to WA RTs for obtaining their perceptions of PACS competence and educational issues. Descriptive (percentage of frequency, mean and standard deviation) and inferential statistics (t test and analysis of variance) were used to analyze the responses of the multiple choice and five-point scale questions from the returned questionnaires. The questionnaire response rate was 57.7 % (173 out of 300). The mean values of all PACS competence questions except questions 2e–g are in the range of 3.9–4.9, i.e., around competent to very competent. Participants indicated they received adequate PACS training (mean 3.8). Statistically significant variables influencing RTs’ perceptions of their PACS competence and educational issues including the age (p < 0.01), gender (p < 0.05), years of practice (p < 0.005–0.05), primary duty (p < 0.05), medical imaging qualification (p < 0.001), general computer skills (p < 0.001), and type of PACS education received (p < 0.001–0.05). The WA RTs indicated that they were competent in using the modality workstation, PACS and radiology information system, and received adequate training. However, future PACS education programs should be tailored to different RTs’ groups. For example, multiple training modules might be necessary to support the PACS competence development of older RTs and those with lower general computer literacy

Production of benzylisoquinoline alkaloids in Saccharomyces cerevisiae

The benzylisoquinoline alkaloids (BIAs) are a diverse class of metabolites that exhibit a broad range of pharmacological activities and are synthesized through plant biosynthetic pathways comprised of complex enzyme activities and regulatory strategies. We have engineered yeast to produce the key intermediate reticuline and downstream BIA metabolites from a commercially available substrate. An enzyme tuning strategy was implemented that identified activity differences between variants from different plants and determined optimal expression levels. By synthesizing both stereoisomer forms of reticuline and integrating enzyme activities from three plant sources and humans, we demonstrated the synthesis of metabolites in the sanguinarine/berberine and morphinan branches. We also demonstrated that a human P450 enzyme exhibits a novel activity in the conversion of (R)-reticuline to the morphinan alkaloid salutaridine. Our engineered microbial hosts offer access to a rich group of BIA molecules and associated activities that will be further expanded through synthetic chemistry and biology approaches

The First Post-Kepler Brightness Dips of KIC 8462852

We present a photometric detection of the first brightness dips of the unique variable star KIC 8462852 since the end of the Kepler space mission in 2013 May. Our regular photometric surveillance started in October 2015, and a sequence of dipping began in 2017 May continuing on through the end of 2017, when the star was no longer visible from Earth. We distinguish four main 1-2.5% dips, named "Elsie," "Celeste," "Skara Brae," and "Angkor", which persist on timescales from several days to weeks. Our main results so far are: (i) there are no apparent changes of the stellar spectrum or polarization during the dips; (ii) the multiband photometry of the dips shows differential reddening favoring non-grey extinction. Therefore, our data are inconsistent with dip models that invoke optically thick material, but rather they are in-line with predictions for an occulter consisting primarily of ordinary dust, where much of the material must be optically thin with a size scale <<1um, and may also be consistent with models invoking variations intrinsic to the stellar photosphere. Notably, our data do not place constraints on the color of the longer-term "secular" dimming, which may be caused by independent processes, or probe different regimes of a single process

A genomic infection control study for Staphylococcus aureus in two Ghanaian hospitals

Eric S Donkor,1 Dorota Jamrozy,2 Richael O Mills,3,4 Thomas Dankwah,3 Philip K Amoo,5 Beverly Egyir,6 Ebenezer V Badoe,7 Joana Twasam,8 Stephen D Bentley2 1Department of Medical Microbiology, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Accra, Ghana; 2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; 3Central Laboratory, Korle-Bu Teaching Hospital, Accra, Ghana; 4Department of Biomedical Sciences, University of Cape Coast, Cape Coast Ghana; 5Public Health Unit, Korle-Bu Teaching Hospital, Accra, Ghana; 6Bacteriology Unit, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana; 7Department of Child Health, School of Medicine and Dentistry, University of Ghana, Accra, Ghana; 8Laboratory Unit, Lekma Hospital, Accra, Ghana Background: Whole genome sequencing analysis (WGSA) provides the best resolution for typing of bacterial isolates and has the potential for identification of transmission pathways. The aim of the study was to apply WGSA to elucidate the possible transmission events involved in two suspected Staphylococcus aureus hospital outbreaks in Ghana and describe genomic features of the S. aureus isolates sampled in the outbreaks. Methods: The study was carried out at Korle-Bu Teaching Hospital and Lekma Hospital where the suspected outbreaks occurred in 2012 and 2015, respectively. The S. aureus isolates collected from the two hospitals were from three sources including carriage, invasive disease, and the environment. Whole genome sequencing of the S. aureus isolates was performed and the sequence reads were mapped to the S. aureus reference genome of strain USA300_FPR3757. A maximum-likelihood phylogenetic tree was reconstructed. Multilocus sequence typing together with the analysis of antimicrobial resistance and virulence genes were performed by short read mapping using the SRST2. Results: The S. aureus isolates belonged to diverse sequence types (STs) with ST15 and ST152 most common. All isolates carried the blaZ gene, with low prevalence of tetK and dfrG genes also observed. All isolates were mecA negative. The pvl genes were common and observed in distinct lineages that revealed diverse Sa2int phages. At Korle-Bu Teaching Hospital, the genomics data indicated several transmission events of S. aureus ST15 involving contamination of various surfaces in the pediatric emergency ward where the outbreak occurred. Conclusion: The pattern of dissemination of the ST15 clone in the emergency ward of Korle-Bu Teaching Hospital highlights a basic problem with disinfection of environmental surfaces at the hospital. Diverse phage population rather than a single highly transmissible phage type likely mediates the high prevalence of pvl genes among the S. aureus isolates. Keywords: Staphylococcus aureus, sequencing, transmission, outbreak, Ghan