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Team:Wageningen UR/Notebook
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<h3>Expanding the database</h3> | <h3>Expanding the database</h3> | ||
| - | <p class="date"> | + | <p class="date">05.08.2013</p> |
<p> In order to expand the database, more information on secondary metabolite backbone enzymes from Aspergilli needs to be added. Luckily there is a recent publication on secondary metabolites from A. nidulans, A. fumigatus, A. niger and A. oryzae. <br /> <br /> | <p> In order to expand the database, more information on secondary metabolite backbone enzymes from Aspergilli needs to be added. Luckily there is a recent publication on secondary metabolites from A. nidulans, A. fumigatus, A. niger and A. oryzae. <br /> <br /> | ||
- D.O. Inglis et al., 2013. <i> Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae. </i> BMC Microbiology, Vol. 13, p. 1-23. | - D.O. Inglis et al., 2013. <i> Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae. </i> BMC Microbiology, Vol. 13, p. 1-23. | ||
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<div class="content"> | <div class="content"> | ||
<h3>Metabolic modeling</h3> | <h3>Metabolic modeling</h3> | ||
| - | <p class="date"> | + | <p class="date">30.07.2013</p> |
<p> The current metabolic model of A. niger needs to be expanded to include the lovastatin pathway as known from literature. First the model has to be checked: is it balanced? can we perform a FBA on the current model? <br /> <br /> | <p> The current metabolic model of A. niger needs to be expanded to include the lovastatin pathway as known from literature. First the model has to be checked: is it balanced? can we perform a FBA on the current model? <br /> <br /> | ||
- M.R. Anderson et al., 2008. <i> Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. </i> Molecular Systems Biology, Vol. 4, Article number 178; doi:10.1038/msb.2008.12 | - M.R. Anderson et al., 2008. <i> Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. </i> Molecular Systems Biology, Vol. 4, Article number 178; doi:10.1038/msb.2008.12 | ||
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<div class="content"> | <div class="content"> | ||
<h3>Metabolic activity: GFP</h3> | <h3>Metabolic activity: GFP</h3> | ||
| - | <p class="date"> | + | <p class="date">24.07.2013</p> |
<p> In a similar way that the DAPI stained cells give an indication of metabolic activity by showing an increase in nuclei, GFP-transformed A. niger also give an indication of metabolic activity by giving an indication on whether transcription and translation occur. | <p> In a similar way that the DAPI stained cells give an indication of metabolic activity by showing an increase in nuclei, GFP-transformed A. niger also give an indication of metabolic activity by giving an indication on whether transcription and translation occur. | ||
</p> | </p> | ||
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<div class="content"> | <div class="content"> | ||
<h3>Database design</h3> | <h3>Database design</h3> | ||
| - | <p class="date"> | + | <p class="date">16.07.2013</p> |
<p> text here | <p> text here | ||
</p> | </p> | ||
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<div class="content"> | <div class="content"> | ||
<h3>DAPI staining</h3> | <h3>DAPI staining</h3> | ||
| - | <p class="date"> | + | <p class="date">11.07.2013</p> |
<p> It has been found that dormant conidia are predominantly bi-nucleate (85%), the remainder being uni-nucleate. Therefore, if one stains the giant cells with DAPI, which colours the nuclei, one can assess whether the nuclei within the cells are actively dividing. This appears to be the the case and thus indicates that the cells are not in a vegetative state. | <p> It has been found that dormant conidia are predominantly bi-nucleate (85%), the remainder being uni-nucleate. Therefore, if one stains the giant cells with DAPI, which colours the nuclei, one can assess whether the nuclei within the cells are actively dividing. This appears to be the the case and thus indicates that the cells are not in a vegetative state. | ||
</p> | </p> | ||
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<div class="content"> | <div class="content"> | ||
<h3>Database planning</h3> | <h3>Database planning</h3> | ||
| - | <p class="date"> | + | <p class="date">01.07.2013</p> |
<p> text here <br /> <br /> | <p> text here <br /> <br /> | ||
- J.F. Sanchez et al., 2012. <i> Advances in Aspergillus secondary metabolite research in the post-genomic era. </i> Nat. Prod. Rep. Vol. 29, p. 351-371 | - J.F. Sanchez et al., 2012. <i> Advances in Aspergillus secondary metabolite research in the post-genomic era. </i> Nat. Prod. Rep. Vol. 29, p. 351-371 | ||
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<div class="content"> | <div class="content"> | ||
<h3>Calcofluor staining</h3> | <h3>Calcofluor staining</h3> | ||
| - | <p class="date"> | + | <p class="date">24.08.2013</p> |
<p> text here | <p> text here | ||
</p> | </p> | ||
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<div class="content"> | <div class="content"> | ||
<h3>Finding the right conditions for distinct phenotypes</h3> | <h3>Finding the right conditions for distinct phenotypes</h3> | ||
| - | <p class="date"> | + | <p class="date">22.06.2013</p> |
<p> As described in literature, N593 formed giant cells after 24h at 44C. Since transcriptome data on N400 from multiple stages in its life cycle is available, this strain is chosen such that this research complements the current RNA landscape profile of A. niger and allows for comparison of data from different life stages. However, unlike N400, N593 repeatedly formed mycelium at 44C. To overcome this effect the temperature was increased to 45C, at which a single cell phenotype was obtained for N593. | <p> As described in literature, N593 formed giant cells after 24h at 44C. Since transcriptome data on N400 from multiple stages in its life cycle is available, this strain is chosen such that this research complements the current RNA landscape profile of A. niger and allows for comparison of data from different life stages. However, unlike N400, N593 repeatedly formed mycelium at 44C. To overcome this effect the temperature was increased to 45C, at which a single cell phenotype was obtained for N593. | ||
</p> | </p> | ||
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<div class="content"> | <div class="content"> | ||
<h3>Host Engineering: Research plan</h3> | <h3>Host Engineering: Research plan</h3> | ||
| - | <p class="date"> | + | <p class="date">13.06.2013</p> |
<p> Different environmental conditions induce changes in phenotypic cellularity of Aspergillus niger. Mapping reads onto the reference genome allows for discovery of patterns in gene expression that are unique to the single cell phenotype. | <p> Different environmental conditions induce changes in phenotypic cellularity of Aspergillus niger. Mapping reads onto the reference genome allows for discovery of patterns in gene expression that are unique to the single cell phenotype. | ||
</p> | </p> | ||
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<div class="content"> | <div class="content"> | ||
<h3>Host Engineering: Research Question</h3> | <h3>Host Engineering: Research Question</h3> | ||
| - | <p class="date"> | + | <p class="date">04.06.2013</p> |
<p> | <p> | ||
Research question: <br /> | Research question: <br /> | ||
Revision as of 23:47, 22 August 2013
- Safety introduction
- General safety
- Fungi-related safety
- Biosafety Regulation
- Safety Improvement Suggestions
- Safety of the Application
- Lablog
- Experimental protocols
notebook entries
Week 12
August (19.08 - 25.08)
Working on the Wiki
20.08.2013
Today the entire team learned how to edit content on the wiki, with special focus on the notebook. Other objectives are to look for icons that can be used in the menu bar and to put up pieces in the team pages
G-blocks from IDT arrived today
19.08.2013
Today the G-blocks we ordered finally arrived! This is great news, because now we can start on the gibson assembly and transformations.
Lovastatin Pathway
19.08.2013
The lovastatin pathway has been added to the metabolic model of Aspergillus niger. Because the medium composition of the model is not yet properly defined, the maximum flux towards lovastatin can be achieved. This however is not realistic and therefore the next thing is to redefined the medium composition.
- B.D. Ames et al., 2011. Crystal structure and biochemical studies of the trans-acting polyketide enoyl reductase LovC from lovastatin biosynthesis. PNAS, doi/10.1073/pnas.1113029109
Week 11
August (12.08 - 18.08)
Title
00.00.2013
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
Title
00.00.2013
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
Week 10
August (05.08 - 11.08)
Expanding the database
05.08.2013
In order to expand the database, more information on secondary metabolite backbone enzymes from Aspergilli needs to be added. Luckily there is a recent publication on secondary metabolites from A. nidulans, A. fumigatus, A. niger and A. oryzae.
- D.O. Inglis et al., 2013. Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae. BMC Microbiology, Vol. 13, p. 1-23.
Week 9
July (29.07 - 04.08)
Metabolic modeling
30.07.2013
The current metabolic model of A. niger needs to be expanded to include the lovastatin pathway as known from literature. First the model has to be checked: is it balanced? can we perform a FBA on the current model?
- M.R. Anderson et al., 2008. Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Molecular Systems Biology, Vol. 4, Article number 178; doi:10.1038/msb.2008.12
Week 8
July (22.07 - 28.07)
Metabolic activity: GFP
24.07.2013
In a similar way that the DAPI stained cells give an indication of metabolic activity by showing an increase in nuclei, GFP-transformed A. niger also give an indication of metabolic activity by giving an indication on whether transcription and translation occur.
Week 7
July (15.07 - 21.07)
Database design
16.07.2013
text here
Week 6
July (08.07 - 14.07)
DAPI staining
11.07.2013
It has been found that dormant conidia are predominantly bi-nucleate (85%), the remainder being uni-nucleate. Therefore, if one stains the giant cells with DAPI, which colours the nuclei, one can assess whether the nuclei within the cells are actively dividing. This appears to be the the case and thus indicates that the cells are not in a vegetative state.
Week 5
July (01.07 - 07.07)
Database planning
01.07.2013
text here
- J.F. Sanchez et al., 2012. Advances in Aspergillus secondary metabolite research in the post-genomic era. Nat. Prod. Rep. Vol. 29, p. 351-371
Week 4
June (24.06 - 30.06)
Calcofluor staining
24.08.2013
text here
Week 3
June (17.06 - 23.06)
Finding the right conditions for distinct phenotypes
22.06.2013
As described in literature, N593 formed giant cells after 24h at 44C. Since transcriptome data on N400 from multiple stages in its life cycle is available, this strain is chosen such that this research complements the current RNA landscape profile of A. niger and allows for comparison of data from different life stages. However, unlike N400, N593 repeatedly formed mycelium at 44C. To overcome this effect the temperature was increased to 45C, at which a single cell phenotype was obtained for N593.
Week 2
June (10.06 - 16.06)
Host Engineering: Research plan
13.06.2013
Different environmental conditions induce changes in phenotypic cellularity of Aspergillus niger. Mapping reads onto the reference genome allows for discovery of patterns in gene expression that are unique to the single cell phenotype.
Week 1
June (03.06 - 09.06)
Host Engineering: Research Question
04.06.2013
Research question:
Finding sets of candidate genes causative to the single cell phenotype in Aspergillus niger by transcriptome analysis.
Subquestions:
- is A. niger metabolically active at 44C?
- does A. niger divide at 44C?
May
Host Engineering: why?
20.08.2013
The single-cell phenotype Aspergillus has a higher surface to volume ratio and results in a lower viscosity of the liquid broth, offering perspective on substantially increasing process yields when used in liquid fermentations. Besides from an industrial point of view it is also interesting from an evolutionary perspective, which couples application-oriented research using a directed evolution approach to a more fundamental research topic: the evolution of multicellularity.
April
Influence of temperature on germination
20.08.2013
A paper from 1970 shows that at 44C Aspergillus niger does not germinate, but rather forms giant cells. This dimorphism is not unfamiliar within the fungal world, where at lower temperatures the mycelium is formed and at higher temperatures the yeast-like form is found.
Anderson, J. G. and J. E. Smith (1972). "Effects of Elevated-Temperatures on Spore Swelling and Germination in Aspergillus Niger." Canadian Journal of Microbiology 18(3): 289-297.
March
February
January
Title
00.00.2013
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
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