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Recent Activity
All posts created by jdaft@leeuniversity.edu
| Link to this post | posted 11 Mar, 2024 13:49 | |
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We did a Gram stain and it appears that the organism is Gram (-). We're not dismissing that it could be archaea, but we haven't looked into what it would take to confirm that. |
Posted in: Phage Discovery/Isolation → Top Agar contamination
| Link to this post | posted 11 Mar, 2024 13:46 | |
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PYCa plate inoculated with contaminated top agar and incubated at 28C. |
1.28MbPosted in: Phage Discovery/Isolation → Top Agar contamination
| Link to this post | posted 11 Mar, 2024 13:46 | |
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PYCa plate inoculated with contaminated top agar and incubated at 60C. |
1.42MbPosted in: Phage Discovery/Isolation → Top Agar contamination
| Link to this post | posted 23 Feb, 2024 21:50 | |
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Has anyone ever had an issue with thermophile contamination in their top agar? We've cultured the thermophile to a PYCa plate and growth only occurs at 60C and not 37C. We think we narrowed it down to our calcium chloride and/or dextrose. Both were remade and filtered and we still are having contamination issues. Our host bacteria is M. foliorum, so our thermophile doesn't appear to be interfering with it's growth, but we still don't like have another bacteria in there with our host culture. ~Joe |
Posted in: Phage Discovery/Isolation → Top Agar contamination
| Link to this post | posted 12 Jan, 2023 17:02 | |
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Thanks Debbie! |
| Link to this post | posted 12 Jan, 2023 15:00 | |
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So for gene 32 (start: 25887 stop: 27365) NCBI blasts is showing strong hits for "Minor Tail Protein), but HHpred is showing strong hits for "Beta-lactamase". Here is my HHpred link: https://toolkit.tuebingen.mpg.de/jobs/1188359. Maroc7 and PherrisBueller, also in the A1 cluster are calling "minor tail protein", but wouldn't these conflicting calls between NCBI/HHpred lead to a "hypothetical" call? Surrounding genes, have some "minor protein" hits, but are mostly "hypothetical". Thanks, Joe |
| Link to this post | posted 11 Jan, 2023 19:45 | |
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I was just curious as to what additional evidence I need to call a protein a "helix-turn-helix DNA binding domain, MerR-like" vs just a "helix-turn-helix DNA binding domain"? I'm including a link to my HHpred hit https://toolkit.tuebingen.mpg.de/jobs/9384933, it shows up as the second hit. NCBI blast just shows up as a helix-turn-helix dna binding domain. Is there some other tool I can use to make the call between the two? I know HTH dna binding domain is the safe call. |
Posted in: Annotation → helix-turn-helix binding domain or protein?