| 1. |
- Aili, Margareta, et al.
(author)
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GAP activity of Yersinia YopE
- 2002
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In: Methods in Enzymology. - 0076-6879 .- 1557-7988. ; 358, s. 359-70
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Journal article (peer-reviewed)
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| 2. |
- Aspholm, Marina, et al.
(author)
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Helicobacter pylori adhesion to carbohydrates
- 2006
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In: Methods in Enzymology. - 0076-6879 .- 1557-7988. ; 417, s. 293-339
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Journal article (peer-reviewed)abstract
- Adherence of bacterial pathogens to host tissues contributes to colonization and virulence and typically involves specific interactions between bacterial proteins called adhesins and cognate oligosaccharide (glycan) or protein motifs in the host that are used as receptors. A given pathogen may have multiple adhesins, each specific for a different set of receptors and, potentially, with different roles in infection and disease. This chapter provides strategies for identifying and analyzing host glycan receptors and the bacterial adhesins that exploit them as receptors, with particular reference to adherence of the gastric pathogen Helicobacter pylori.
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| 3. |
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| 4. |
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| 5. |
- Borga, Magnus, et al.
(author)
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Brown adipose tissue in humans: detection and functional analysis using PET (positron emission tomography), MRI (magnetic resonance imaging), and DECT (dual energy computed tomography).
- 2014
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In: Methods in enzymology. - : Elsevier. - 1557-7988. ; 537, s. 141-59, s. 141-159
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Journal article (peer-reviewed)abstract
- If the beneficial effects of brown adipose tissue (BAT) on whole body metabolism, as observed in nonhuman experimental models, are to be translated to humans, tools that accurately measure how BAT influences human metabolism will be required. This chapter discusses such techniques, how they can be used, what they can measure and also some of their limitations. The focus is on detection and functional analysis of human BAT and how this can be facilitated by applying advanced imaging technology such as positron emission tomography, magnetic resonance imaging, and dual energy computed tomography.
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| 6. |
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| 7. |
- Budayova-Spano, Monika, et al.
(author)
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Large crystal growth for neutron protein crystallography
- 2020
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In: Neutron Crystallography in Structural Biology. - : Elsevier. - 1557-7988 .- 0076-6879. ; 634, s. 21-46
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Book chapter (peer-reviewed)abstract
- The use of neutron protein crystallography (NPX) is expanding rapidly, with most structures determined in the last decade. This growth is stimulated by a number of developments, spanning from the building of new NPX beamlines to the availability of improved software for structure refinement. The main bottleneck preventing structural biologists from adding NPX to the suite of methods commonly used is the large volume of the individual crystals required for a successful experiment. A survey of deposited NPX structures in the Protein Data Bank shows that about two-thirds came from crystals prepared using vapor diffusion, while batch and dialysis-based methods all-together contribute to most of the remaining one-third. This chapter explains the underlying principles of these protein crystallization methods and provides practical examples that may help others to successfully prepare large crystals for NPX.
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| 8. |
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| 9. |
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| 10. |
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| 11. |
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| 12. |
- Eklof, Jens M., et al.
(author)
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Distinguishing xyloglucanase activity in endo-β(1 → 4)glucanases
- 2012
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In: Methods in Enzymology. - : Elsevier BV. - 0076-6879 .- 1557-7988. - 9780124159310 ; 510, s. 97-120
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Journal article (peer-reviewed)abstract
- The ability of beta-glucanases to cleave xyloglucans, a family of highly decorated beta-glucans ubiquitous in plant biomass, has traditionally been overlooked in functional biochemical studies. An emerging body of data indicates, however, that a spectrum of xyloglucan specificity resides in diverse glycoside hydrolases from a range of carbohydrate-active enzyme families including classic "cellulase" families. This chapter outlines a series of enzyme kinetic and product analysis methods to establish degrees of xyloglucan specificity and modes of action of glycosidases emerging from enzyme discovery projects.
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| 13. |
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| 14. |
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| 15. |
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| 16. |
- Galluzzi, L, et al.
(author)
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Preface
- 2017
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In: Methods in enzymology. - 1557-7988. ; 588, s. XXV-XXXI
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Journal article (other academic/artistic)
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| 17. |
- Galluzzi, L, et al.
(author)
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Preface
- 2017
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In: Methods in enzymology. - 1557-7988. ; 587, s. XXIII-XXIX
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Journal article (other academic/artistic)
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| 18. |
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| 19. |
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| 20. |
- Gyllensten, Ulf, et al.
(author)
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Sequencing of in vitro amplified DNA
- 1993
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In: Methods in Enzymology. - 0076-6879 .- 1557-7988. ; 218, s. 3-16
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Journal article (other academic/artistic)
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| 21. |
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| 22. |
- He, Feng, et al.
(author)
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Chapter 6. Qualitative and quantitative assessment of the activity of the yeast nonsense-mediated mRNA decay pathway.
- 2008
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In: Methods in Enzymology. - 0076-6879 .- 1557-7988. ; 449, s. 127-47
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Journal article (peer-reviewed)abstract
- The yeast Saccharomyces cerevisiae provides an ideal model system for elucidation of the molecular mechanisms that regulate the nonsense-mediated mRNA decay (NMD) pathway. This chapter describes an array of molecular biological, genetic, and biochemical tools that facilitate the characterization of transcripts that comprise NMD substrates and provide insights into the roles of the upf/nmd proteins in mRNA decay and translation termination. Examples illustrate the use of these methods in wild-type and NMD-deficient cells to monitor the abundance, structure, and half-lives of nonsense-containing mRNAs, the read through of premature termination codons by the ribosome, and the positioning of ribosomes at or near normal and premature termination codons.
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| 23. |
- Hebert, Hans, et al.
(author)
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Two-dimensional crystallization and electron crystallography of MAPEG proteins.
- 2005
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In: Methods in Enzymology. - 0076-6879 .- 1557-7988. ; 401, s. 161-8
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Journal article (peer-reviewed)abstract
- Members of the membrane-associated proteins in the eicosanoid and glutathione metabolism (MAPEG) superfamily have been subjected to two-dimensional crystallization experiments. A common denominator for successful attempts has been the use of a low lipid/protein ratio in the range of 1-9 (mol/mol). Electron crystallography demonstrated either hexagonal or orthorhombic packing of trimeric protein units. Three-dimensional structure analysis of the MAPEG member microsomal glutathione transferase 1 has shown that the monomer for this protein contains a left-handed bundle of four transmembrane helices. It is likely that this is a common structural motif for MAPEG proteins, because projection maps of all structurally characterized members are very similar.
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| 24. |
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| 25. |
- Heidorn, Thorsten, et al.
(author)
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Synthetic Biology in Cyanobacteria : Engineering and Analyzing Novel Functions
- 2011
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In: Methods in Enzymology. - 0076-6879 .- 1557-7988. ; 497, s. 539-579
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Research review (peer-reviewed)abstract
- Cyanobacteria are the only prokaryotes capable of using sunlight as their energy, water as an electron donor, and air as a source of carbon and, for some nitrogen-fixing strains, nitrogen. Compared to algae and plants, cyanobacteria are much easier to genetically engineer, and many of the standard biological parts available for Synthetic Biology applications in Escherichia coli can also be used in cyanobacteria. However, characterization of such parts in cyanobacteria reveals differences in performance when compared to E. coli, emphasizing the importance of detailed characterization in the cellular context of a biological chassis. Furthermore, cyanobacteria possess special characteristics (e.g., multiple copies of their chromosomes, high content of photosynthetically active proteins in the thylakoids, the presence of exopolysaccharides and extracellular glycolipids, and the existence of a circadian rhythm) that have to be taken into account when genetically engineering them. With this chapter, the synthetic biologist is given an overview of existing biological parts, tools and protocols for the genetic engineering, and molecular analysis of cyanobacteria for Synthetic Biology applications.
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