SEA-PHAGES | All posts created by DanRussell

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Link to this post \| posted 08 Mar, 2024 00:32
DanRussell	Way back in our "60 phage paper", we grouped phages into clusters based on > 50% nucleotide similarity. Of course, exactly what "50% nucleotide similarity" meant depended on which metrics in particular you looked at, so we used several different ones. You can read about them in the paper. More recently, we've moved to comparing genes rather than nucleotides, and have used ~35% Gene Content Similarity to put phages into clusters. Now, we're probably moving towards using a metric called Protein Equivalence Quotient to cluster phages. It's an ongoing process, and there is no "right" answer and phages will always challenge us by not neatly fitting into bins. PhamClust paper There have been a few groups who have looked at geography, and though there doesn't seem to be any high-level correlation between geography and type of phages found, some subclusters or even genes have only been found in certain geographical areas. –Dan

Link to this post | posted 08 Mar, 2024 00:32

Way back in our "60 phage paper", we grouped phages into clusters based on > 50% nucleotide similarity. Of course, exactly what "50% nucleotide similarity" meant depended on which metrics in particular you looked at, so we used several different ones. You can read about them in the paper.

More recently, we've moved to comparing genes rather than nucleotides, and have used ~35% Gene Content Similarity to put phages into clusters.

Now, we're probably moving towards using a metric called Protein Equivalence Quotient to cluster phages. It's an ongoing process, and there is no "right" answer and phages will always challenge us by not neatly fitting into bins.
PhamClust paper

There have been a few groups who have looked at geography, and though there doesn't seem to be any high-level correlation between geography and type of phages found, some subclusters or even genes have only been found in certain geographical areas.

–Dan

Posted in: Phage Biology → Phage Clustering

Link to this post \| posted 13 Feb, 2024 14:57
DanRussell	eagodin Thanks for the update, Debbie! Does this mean that we shouldn't use Atuin, Mimi, or Racecar as comparators at all, since the sequences were incorrect? I think my students are up for a good challenge, but will certainly reach out with any questions that come up. Liz Hi Liz, Just to be clear, the sequences were correct in the sense that all the bases were right. The change was just where Base 1 was, and duplicating a portion of the genome. (Not changing any individual bases or anything.) So everything should be fine/comparable, including the original annotations of those complete ones, but numbers will have changed. –Dan

Link to this post | posted 13 Feb, 2024 14:57

DanRussell

eagodin
Thanks for the update, Debbie! Does this mean that we shouldn't use Atuin, Mimi, or Racecar as comparators at all, since the sequences were incorrect? I think my students are up for a good challenge, but will certainly reach out with any questions that come up.
Liz

Hi Liz,

Just to be clear, the sequences were correct in the sense that all the bases were right. The change was just where Base 1 was, and duplicating a portion of the genome. (Not changing any individual bases or anything.) So everything should be fine/comparable, including the original annotations of those complete ones, but numbers will have changed.

–Dan

Posted in: Phamerator → Cluster FC in Phamerator

Link to this post \| posted 08 Feb, 2024 19:31
DanRussell	Hi Nancy, Can you post the file here perhaps? Thanks, –Dan

Posted in: DNA Master → Error when opening FASTA file

Link to this post \| posted 10 Jan, 2024 21:38
DanRussell	jcaoyao@gmail.com Most thankful for your wonderful explanation, Dan! It does make sense. So having a Class 2 Biosafety Cabinet wouldn't make your lab a BSL2, and therefore, allow you to handle M. abscessus? Right, it's definitely more complicated than that! (At least for us at Pitt.)

Posted in: Mycobacterium → Legal statement

Link to this post \| posted 10 Jan, 2024 21:18
DanRussell	Hi Juan Carlos, Here in the Hatfull Lab at the University of Pittsburgh, all of our clinical M. abscessus isolates are classified as BSL-2, and for good reason. Sometimes an apparently "healthy human" may have undiagnosed or non-obvious issues, and treating an opportunistic pathogen as "harmless" is dangerous. As for the "ultimate, legal, foolproof" statement, that probably doesn't exist. BSL guidelines are set by your institution, and we at Pitt follow guidelines set by Pitt, the CDC, NIH, strain collections, etc. Different schools, countries, or organizations may have different rules, but we always expect all SEA-PHAGES schools to abide by appropriate BSL regulations in their region. We've had real safety concerns recently, as some SEA-PHAGES schools have tried phagehunting on bacteria they've isolated from the environment. While this offer a different phage yield, allowing students to work with an unknown bacterium and treating it as BSL-1 is not endorsed by the SEA-PHAGES program! –Dan Edited 10 Jan, 2024 21:37

Link to this post | posted 10 Jan, 2024 21:18

DanRussell

Hi Juan Carlos,

Here in the Hatfull Lab at the University of Pittsburgh, all of our clinical M. abscessus isolates are classified as BSL-2, and for good reason. Sometimes an apparently "healthy human" may have undiagnosed or non-obvious issues, and treating an opportunistic pathogen as "harmless" is dangerous.

As for the "ultimate, legal, foolproof" statement, that probably doesn't exist. BSL guidelines are set by your institution, and we at Pitt follow guidelines set by Pitt, the CDC, NIH, strain collections, etc. Different schools, countries, or organizations may have different rules, but we always expect all SEA-PHAGES schools to abide by appropriate BSL regulations in their region.

We've had real safety concerns recently, as some SEA-PHAGES schools have tried phagehunting on bacteria they've isolated from the environment. While this offer a different phage yield, allowing students to work with an unknown bacterium and treating it as BSL-1 is not endorsed by the SEA-PHAGES program!

–Dan

Edited 10 Jan, 2024 21:37

Posted in: Mycobacterium → Legal statement

Link to this post \| posted 03 Nov, 2023 16:47
DanRussell	Hi SEA-PHAGES faculty folks, We got the following message and wanted to pass it on to you in case you're looking for potential summer employment. "The Summer Science Program recently designed a program in bacterial genomics where participants evolve a BSL1 bacteria (V. natriegens) to tolerate ever-increasing levels of antibiotics. After the evolution and Illumina sequencing our participants assemble the genome and try to identify putative beneficial mutations. We are looking for faculty to lead the micro and the bioinformatics sides, and Phage Hunters seemed like a good place to find faculty." Details on their employment page: https://summerscience.org/employment/ –Dan

Link to this post | posted 03 Nov, 2023 16:47

DanRussell

Hi SEA-PHAGES faculty folks,

We got the following message and wanted to pass it on to you in case you're looking for potential summer employment.

"The Summer Science Program recently designed a program in bacterial genomics where participants evolve a BSL1 bacteria (V. natriegens) to tolerate ever-increasing levels of antibiotics. After the evolution and Illumina sequencing our participants assemble the genome and try to identify putative beneficial mutations. We are looking for faculty to lead the micro and the bioinformatics sides, and Phage Hunters seemed like a good place to find faculty."

Details on their employment page:
https://summerscience.org/employment/

–Dan

Posted in: General Message Board → Summer Faculty Job Opportunity

Link to this post \| posted 19 Jul, 2023 14:35
DanRussell	jcaoyao@gmail.com Hello Staff, I can't move files from my computer to the VM, so I tried clicking "Insert Guest Additions CD Image…", but nothing happened, no activity occurred in the terminal window or anywhere. What could I do, please? Thank you. Hi, you can try opening a terminal and running this command: `sudo apt-get install virtualbox-guest-utils` If that doesn't work, I'd suggest asking the internet! –Dan

Link to this post | posted 19 Jul, 2023 14:35

DanRussell

jcaoyao@gmail.com
Hello Staff, I can't move files from my computer to the VM, so I tried clicking "Insert Guest Additions CD Image…", but nothing happened, no activity occurred in the terminal window or anywhere. What could I do, please? Thank you.

Hi, you can try opening a terminal and running this command:

sudo apt-get install virtualbox-guest-utils

If that doesn't work, I'd suggest asking the internet!

–Dan

Posted in: Phamerator → Install Guest Additions to VM ---- Without "SEAFaculty Login ability"

Link to this post \| posted 06 Jun, 2023 15:45
DanRussell	afreise Hi Dan - could we get a new forum for Cluster FP phages? Of course! Here you go: https://seaphages.org/forums/forum/222/ –Dan

Posted in: Cluster-Specific Annotation Tips → Using This Forum

Link to this post \| posted 27 Jan, 2023 18:06
DanRussell	From Eric Miller: We are still recruiting undergraduates for the forthcoming summer 2023 REEU BeeMORE (Bees and Microbes) program at NC State University. Our goal is to recruit as many students underrepresented in agriculture and science as possible; our participants are selected based on their motivation to learn and to make the most of our 9 week program. Undergraduates in their second or third year are preferred, with most of them coming from outside the NC State University community. Here is the link to our home page: https://harvest.cals.ncsu.edu/beemore/ On the web page there is a recent video describing the program, a flyer suitable for printing or sharing electronically, and a link to the brief application procedure. We expect to keep the application window open for a bit longer. The program is funded for at least the next four years. Please share broadly! Thank you for helping get the word out, to your students and to your colleagues. Post it on one of your web pages citing summer opportunities! Thank you and all the best, Eric

Link to this post | posted 27 Jan, 2023 18:06

DanRussell

From Eric Miller:

We are still recruiting undergraduates for the forthcoming summer 2023 REEU BeeMORE (Bees and Microbes) program at NC State University. Our goal is to recruit as many students underrepresented in agriculture and science as possible; our participants are selected based on their motivation to learn and to make the most of our 9 week program. Undergraduates in their second or third year are preferred, with most of them coming from outside the NC State University community.

Here is the link to our home page: https://harvest.cals.ncsu.edu/beemore/

On the web page there is a recent video describing the program, a flyer suitable for printing or sharing electronically, and a link to the brief application procedure. We expect to keep the application window open for a bit longer. The program is funded for at least the next four years.

Please share broadly! Thank you for helping get the word out, to your students and to your colleagues. Post it on one of your web pages citing summer opportunities!

Thank you and all the best,
Eric

Posted in: General Message Board → Undergrad Summer Bees Program at NC State

Link to this post \| posted 19 Jan, 2023 14:47
DanRussell	Hi Alison, Thanks. I asked because if they're the newer "M1" Macs, then we don't necessarily have a recommended way forward. (The chip architecture on the M1 Macs is different than the old Intel ones, and so VirtualBox will likely never work on M1s.) That said, if M1 is the issue, there's a big thread here on that: https://seaphages.org/forums/topic/5256/ –Dan

Posted in: SEA-PHAGES Virtual Machine → Meditation guru error message - See Community Section

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