| 1. |
- Alalam, Hanna, et al.
(författare)
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Conjugation factors controlling F-plasmid antibiotic resistance transmission
- 2018
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Ingår i: BioRxiv. - : Cold Spring Harbor Laboratory.
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The rapid horizontal transmission of many antibiotic resistance genes between bacterial host cells on conjugative plasmids is a major cause of the accelerating antibiotic resistance crisis. Preventing understanding and targeting conjugation, there currently are no experimental platforms for fast and cost-efficient screening of genetic effects on antibiotic resistance transmission by conjugation. We introduce a novel experimental framework to screen for conjugation based horizontal transmission of antibiotic resistance between >60,000 pairs of cell populations in parallel. Plasmid-carrying donor strains are constructed in high throughput. We then mix the resistance plasmid carrying donors with recipients in a design where only transconjugants can reproduce, measure growth in dense intervals and extract transmission times as the growth lag. As proof-of-principle, we exhaustively explored chromosomal genes controlling F plasmid donation within E. coli populations, by screening the Keio deletion collection at high replication. We recover all six known chromosomal gene mutants affecting conjugation and identify >50 novel factors, all of which diminish antibiotic resistance transmission. We verify 10 of the novel genes' effects in a liquid mating assay. The new framework holds great potential for exhaustive disclosing of candidate targets for helper drugs that delay resistance development in patients and societies and improves the longevity of current and future antibiotics.
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| 2. |
- Farewell, Anne, 1961
(författare)
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Rising to the Top: Promoting Deeper Learning in the Laboratory
- 2018
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Ingår i: National Center for Case Study Teaching in Science.
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Bokkapitel (refereegranskat)abstract
- Inquiry-based labs differ from cookbook labs in that inquiry-based labs contain an element of experimentation. A cookbook lab can be performed by a student without understanding any of the theory connected with the exercise whereas inquiry-based labs require a degree of conceptual knowledge for a student to perform the lab. Inquiry-based labs also strengthen and deepen students understanding of topics discussed in lectures or reading assignments. There are many variations and degrees of inquiry in these labs ranging from a lab that is entirely designed by the students to those that include small questions requiring that the students predict the outcomes of a lab or fill in missing information (guided inquiry). A simple specific example of a cookbook lab would be instructing students to measure volume changes between ice and liquid water. The students would be given step by step instructions to follow and would not need to apply any conceptual knowledge. An inquiry based lab on the same topic would allow the students to design their own experiment to discover how the volume of liquid water differs from that of ice. One goal of this activity is to introduce inquiry-based lab design. Beyond lab design, lab supervision is crucial to encouraging students to use their conceptual knowledge when doing a practical lab. Lab assistants or teachers who are involved in the lab can use student questions to encourage deeper understanding. This case study includes a role-play exercise for this skill. This case study has been designed to be used in science education courses for both graduate student laboratory assistants and lecturers or professors in natural sciences at the university or college level. It includes discussion and role-play of a hypothetical laboratory. No specific knowledge of biology or chemistry is needed beyond high school level to complete this task, though knowledge of the existence of microorganisms (yeast) and proteins is assumed. In addition, this activity is suitable for participants with little or no pedagogics training.
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| 3. |
- Farewell, Anne, 1961
(författare)
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Teaching Science: Design of a Master’s Level Biology Course
- 2015
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Ingår i: Pedagogical Essays, The unit for Pedagogical Development and Interactive Learning (PIL). - Göteborg : University of Gothenburg.
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- In this work, I describe the development of a Master’s level microbiology course which uses an active learning approach to encourage the students to think scientifically about the course material and gives the students training in experimental design, data analysis, literature research and scientific oral and written presentation. The course combines a case study approach with an inquiry based lab. I discuss how the students are formatively assessed in the course and how this becomes a motivational tool. Finally, I discuss the feedback from the students in terms of course evaluation.
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| 4. |
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| 5. |
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| 6. |
- Graf, Fabrice, et al.
(författare)
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Inhibiting conjugation as a tool in the fight against antibiotic resistance
- 2019
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Ingår i: Drug Development Research. - : Wiley. - 0272-4391 .- 1098-2299. ; 80:1, s. 19-23
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Tidskriftsartikel (refereegranskat)abstract
- © 2018 Wiley Periodicals, Inc. (Table presented.). Antibiotic resistance, especially in gram-negative bacteria, is spreading globally and rapidly. Development of new antibiotics lags behind; therefore, novel approaches to the problem of antibiotic resistance are sorely needed and this commentary highlights one relatively unexplored target for drug development: conjugation. Conjugation is a common mechanism of horizontal gene transfer in bacteria that is instrumental in the spread of antibiotic resistance among bacteria. Most resistance genes are found on mobile genetic elements and primarily spread by conjugation. Furthermore, conjugative elements can act as a reservoir to maintain antibiotic resistance in the bacterial population even in the absence of antibiotic selection. Thus, conjugation can spread antibiotic resistance quickly between bacteria of the microbiome and pathogens when selective pressure (antibiotics) is introduced. Potential drug targets include the plasmid-encoded conjugation system and the host-encoded proteins important for conjugation. Ideally, a conjugation inhibitor will be used alongside antibiotics to prevent the spread of resistance to or within pathogens while not acting as a growth inhibitor itself. Inhibiting conjugation will be an important addition to our arsenal of strategies to combat the antibiotic resistance crisis, allowing us to extend the usefulness of antibiotics.
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| 7. |
- Moradigaravand, Danesh, et al.
(författare)
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Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data.
- 2018
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Ingår i: PLoS computational biology. - : Public Library of Science (PLoS). - 1553-7358. ; 14:12
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Tidskriftsartikel (refereegranskat)abstract
- The emergence of microbial antibiotic resistance is a global health threat. In clinical settings, the key to controlling spread of resistant strains is accurate and rapid detection. As traditional culture-based methods are time consuming, genetic approaches have recently been developed for this task. The detection of antibiotic resistance is typically made by measuring a few known determinants previously identified from genome sequencing, and thus requires the prior knowledge of its biological mechanisms. To overcome this limitation, we employed machine learning models to predict resistance to 11 compounds across four classes of antibiotics from existing and novel whole genome sequences of 1936 E. coli strains. We considered a range of methods, and examined population structure, isolation year, gene content, and polymorphism information as predictors. Gradient boosted decision trees consistently outperformed alternative models with an average accuracy of 0.91 on held-out data (range 0.81-0.97). While the best models most frequently employed gene content, an average accuracy score of 0.90 could be obtained using population structure information alone. Single nucleotide variation data were less useful, and significantly improved prediction only for two antibiotics, including ciprofloxacin. These results demonstrate that antibiotic resistance in E. coli can be accurately predicted from whole genome sequences without a priori knowledge of mechanisms, and that both genomic and epidemiological data can be informative. This paves way to integrating machine learning approaches into diagnostic tools in the clinic.
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| 8. |
- Nilsson, Kelly Dimovska, et al.
(författare)
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Chemical Changes On, and Through, The Bacterial Envelope in Escherichia coli Mutants Exhibiting Impaired Plasmid Transfer Identified Using Time-of-Flight Secondary Ion Mass Spectrometry.
- 2019
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Ingår i: Analytical chemistry. - : American Chemical Society (ACS). - 1520-6882 .- 0003-2700. ; 91:17, s. 11355-11361
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Tidskriftsartikel (refereegranskat)abstract
- Time-of-flight secondary ion mass spectrometry (ToF-SIMS) using a (CO2)6k+ gas cluster ion beam (GCIB) was used to analyze Escherichia coli mutants previously identified as having impaired plasmid transfer capability related to the spread of antibiotic resistance. The subset of mutants selected were expected to result in changes in the bacterial envelope composition through the deletion of genes encoding for FabF, DapF, and Lpp, where the surface sensitivity of ToF-SIMS can be most useful. Analysis of arrays of spotted bacteria allowed changes in the lipid composition of the bacteria to be elucidated using multivariate analysis and confirmed through imaging of individual ion signals. Significant changes in chemical composition were observed, including a surprising loss of cyclopropanated fatty acids in the fabF mutant where FabF is associated with the elongation of FA(16:1) to FA(18:1) and not cyclopropane formation. The ability of the GCIB to generate increased higher mass signals from biological samples allowed intact lipid A (m/z 1796) to be detected on the bacteria and, despite a 40 keV impact energy, depth profiled through the bacterial envelope along with other high mass ions including species at m/z 1820 and 2428, attributed to ECACYC, that were only observed below the surface of the bacteria and were notably absent in the depth profile of the lpp mutant. The analysis provides new insights into the action of the specific pathways targeted in this study and paves the way for whole new avenues for the characterization of intact molecules within the bacterial envelope.
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| 10. |
- Thomsen, Hanna, 1989, et al.
(författare)
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Delivery of cyclodextrin polymers to bacterial biofilms - An exploratory study using rhodamine labelled cyclodextrins and multiphoton microscopy
- 2017
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Ingår i: International Journal of Pharmaceutics. - : Elsevier BV. - 0378-5173 .- 1873-3476. ; 531:2, s. 650-657
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Tidskriftsartikel (refereegranskat)abstract
- © 2017 The Authors. Cyclodextrin (CD) polymers are interesting nanoparticulate systems for pharmaceutical delivery; however, knowledge regarding their applications towards delivery into complex microbial biofilm structures is so far limited. The challenge is to demonstrate penetration and transport through the biofilm and its exopolysaccharide matrix. The ideal functionalization for penetration into mature biofilms is unexplored. In this paper, we present a novel set of rhodamine labelled βCD-polymers, with different charge moieties, i.e., neutral, anionic, and cationic, and explore their potential delivery into mature Staphylococcus epidermidis biofilms using multiphoton laser scanning microscopy (MPM). The S. epidermidis biofilms, being a medically relevant model organism, were stained with SYTO9. By using MPM, three-dimensional imaging and spectral investigation of the distribution of the βCD-polymers could be obtained. It was found that the cationic βCD-polymers showed significantly higher integration into the biofilms, compared to neutral and anionic functionalized βCDs. None of the carriers presented any inherent toxicity to the biofilms, meaning that the addition of rhodamine moiety does not affect the inertness of the delivery system. Taken together, this study demonstrates a novel approach by which delivery of fluorescently labelled CD nanoparticles to bacterial biofilms can be explored using MPM. Future studies should be undertaken investigating the potential in using cationic functionalization of CD based delivery systems for targeting anti-microbial effects in biofilms.
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