SEA-PHAGES | All posts created by Tamarah

Link to this post \| posted 13 Jan, 2024 20:08
Tamarah_Adair	Vassie, I was thinking the same thing about the shirts! David, thank you for all the inspiring messages and leadership. I will miss seeing you, but I wish you the very best! Tammy vcw0 Dear David, There is not a word big enough yet in languages I know to account for the impact you have had on the Science Education community and me. I thank you for all the inspiration and advice you provided that powered us forward with this work. I wish you all the peace and adventure you can handle. Just one question remains - what do I do with all the Hawaiian shirts I ordered over the holidays? Best regards, Vassie Vassie Ware Professor, Molecular Biology Lehigh University Bethlehem, PA vcw0@lehigh.edu 172Kb

Link to this post | posted 13 Jan, 2024 20:08

Vassie, I was thinking the same thing about the shirts!

David, thank you for all the inspiring messages and leadership. I will miss seeing you, but I wish you the very best!
Tammy

vcw0
Dear David,

There is not a word big enough yet in languages I know to account for the impact you have had on the Science Education community and me. I thank you for all the inspiration and advice you provided that powered us forward with this work. I wish you all the peace and adventure you can handle. Just one question remains - what do I do with all the Hawaiian shirts I ordered over the holidays?

Best regards,
Vassie

Vassie Ware
Professor, Molecular Biology
Lehigh University
Bethlehem, PA
vcw0@lehigh.edu

Posted in: General Message Board → A Message from David Asai

Link to this post \| posted 15 Sep, 2023 22:01
Tamarah_Adair	Has anyone studied the holins in AZ?

Posted in: Cluster AZ Annotation Tips → Endolysin

Link to this post \| posted 03 Jun, 2023 16:04
Tamarah_Adair	In Lakshmi and other AK phages GeneMark is showing a potential frameshift arrow and coding potential that some students have looked at and hypothesized that there are 2 genes (starting at 31127 and then switching frames at a polyG sequence to end at 31589), and then a second gene at 31589-33757 that make up a primase/polymerase AND a helicase instead of the one larger orf 31127-33757 that combines these domains and is annotated as primase/polymerase/helicase with HHPred evidence. In some draft phages, this long orf (31127-33757 in Lakshmi) appears to have a short overlapping gene about 100bp from the start, representing this extra coding potential that MAY be the second half of the first gene, as hypothesized by these students. (They did some modeling that supports their ideas.) The paper the students have https://www.frontiersin.org/articles/10.3389/fgene.2012.00242/full indicates there could be GGGGG slippery sequence. However, without further evidence (as of June 2023), we are NOT calling these 2 genes or a frameshift at this time, and instead calling the single long orf. Debbie added GeneMark output to illustrate. Agreed that something like what is described could be some sort of frameshift BUT an area of low coding potential that just happens to be higher CP in another frame is not unheard of. Only 1 ORF to call here. Bench data would be required here. Edited 06 Jun, 2023 01:52 185Kb

Link to this post | posted 03 Jun, 2023 16:04

Tamarah_Adair

In Lakshmi and other AK phages GeneMark is showing a potential frameshift arrow and coding potential that some students have looked at and hypothesized that there are 2 genes (starting at 31127 and then switching frames at a polyG sequence to end at 31589), and then a second gene at 31589-33757 that make up a primase/polymerase AND a helicase instead of the one larger orf 31127-33757 that combines these domains and is annotated as primase/polymerase/helicase with HHPred evidence. In some draft phages, this long orf (31127-33757 in Lakshmi) appears to have a short overlapping gene about 100bp from the start, representing this extra coding potential that MAY be the second half of the first gene, as hypothesized by these students. (They did some modeling that supports their ideas.)
The paper the students have https://www.frontiersin.org/articles/10.3389/fgene.2012.00242/full
indicates there could be GGGGG slippery sequence.

However, without further evidence (as of June 2023), we are NOT calling these 2 genes or a frameshift at this time, and instead calling the single long orf.

Debbie added GeneMark output to illustrate. Agreed that something like what is described could be some sort of frameshift BUT an area of low coding potential that just happens to be higher CP in another frame is not unheard of. Only 1 ORF to call here. Bench data would be required here.

Edited 06 Jun, 2023 01:52

Posted in: Cluster AK Annotation Tips → Primase/helicase question

Link to this post \| posted 03 Jun, 2023 16:03
Tamarah_Adair	In Lakshmi and other AK phages GeneMark is showing a potential frameshift arrow and coding potential that some students have looked at and hypothesized that there are 2 genes (starting at 31127 and then switching frames at a polyG sequence to end at 31589), and then a second gene at 31589-33757 that make up a primase/polymerase AND a helicase instead of the one larger orf 31127-33757 that combines these domains and is annotated as primase/polymerase/helicase with HHPred evidence. In some draft phages, this long orf (31127-33757 in Lakshmi) appears to have a short overlapping gene about 100bp from the start, representing this extra coding potential that MAY be the second half of the first gene, as hypothesized by these students. (They did some modeling that supports their ideas.) The paper the students have https://www.frontiersin.org/articles/10.3389/fgene.2012.00242/full indicates there could be GGGGG slippery sequence. However, without further evidence (as of June 2023), we are NOT calling these 2 genes or a frameshift at this time, and instead calling the single long orf.

Link to this post | posted 03 Jun, 2023 16:03

Tamarah_Adair

Posted in: Cluster AK Annotation Tips → Primase/helicase question

Link to this post \| posted 12 Sep, 2022 23:29
Tamarah_Adair	Job openings in the Department of Biology at Baylor University

Posted in: General Message Board → Job Openings at Baylor University

Link to this post \| posted 30 Jul, 2022 17:36
Tamarah_Adair	Hi. I have been using Arthrobacter hosts for several years and I am thinking about trying out hunting for Corynebacteriophage this year. Are there any suggestions for hosts or protocols? Thank you for any information. Tammy

Posted in: Phage Discovery/Isolation → New hosts - human microbiome

Link to this post \| posted 21 May, 2022 13:28
Tamarah_Adair	I was checking my Review to Improve on Casserole and there are changes to gpXX for each hypothetical protein. Is this an update?

Posted in: Notes and Final Files → Hypothetical Proteins in the Product Field

Link to this post \| posted 10 Oct, 2021 21:08
Tamarah_Adair	https://apply.interfolio.com/87932 The Department of Biology (www.baylor.edu/biology) in the College of Arts & Sciences (www.baylor.edu/artsandsciences) seeks applications for a Lecturer position to teach multiple sections of undergraduate Physiology including human anatomy (majors), human physiology (majors) and human anatomy & physiology (allied health). Lecturers are also expected to teach in the undergraduate introductory biology sequence. Lecturers should develop educational strategies that incorporate student-centered learning activities for lecture and innovative curricula for lab courses, and promote a culture of discovery through excellence in teaching. The department has developed and encourages the use of an undergraduate Learning Assistant program to facilitate active learning. While research is not a requirement of the position, the department has future plans to encourage lecturers to participate in course-based undergraduate research experiences. This position is a 10-month appointment during the academic year. Teaching opportunities during summers may be available depending on student demand. Though not a tenure-track position, Regular Lecturers are full-time faculty and are eligible to progress toward the rank of Senior Lecturer. Salary is commensurate with experience and qualifications. Qualifications Successful applicants will hold a Ph.D. or equivalent in a biologically related discipline and will have a track record of developing student-centered learning activities that includes developing course-based undergraduate research experiences or other innovative approaches. The Department of Biology keenly values diversity amongst its faculty and students and believes it is essential to achieving excellence. Application Instructions Applications will be accepted until the position is filled, but to ensure full consideration, complete applications must be submitted by September 30, 2021. To apply, submit a letter of application, a 1-2 page teaching statement, prior research statement, a current curriculum vitae, a copy of an official transcript showing the highest degree conferred (if the Ph.D. is in progress, a copy of the official transcript of completed Ph.D. hours should also be submitted), and names and contact information of 3 individuals that the search committee can contact for letters of recommendation. Inquiries about the position can be sent to Search Committee Chair, Dr. Marcie Moehnke at BioLecturerSearch@baylor.edu.

Link to this post | posted 10 Oct, 2021 21:08

Tamarah_Adair

https://apply.interfolio.com/87932

The Department of Biology (www.baylor.edu/biology) in the College of Arts & Sciences (www.baylor.edu/artsandsciences) seeks applications for a Lecturer position to teach multiple sections of undergraduate Physiology including human anatomy (majors), human physiology (majors) and human anatomy & physiology (allied health). Lecturers are also expected to teach in the undergraduate introductory biology sequence.

Lecturers should develop educational strategies that incorporate student-centered learning activities for lecture and innovative curricula for lab courses, and promote a culture of discovery through excellence in teaching. The department has developed and encourages the use of an undergraduate Learning Assistant program to facilitate active learning. While research is not a requirement of the position, the department has future plans to encourage lecturers to participate in course-based undergraduate research experiences.

This position is a 10-month appointment during the academic year. Teaching opportunities during summers may be available depending on student demand. Though not a tenure-track position, Regular Lecturers are full-time faculty and are eligible to progress toward the rank of Senior Lecturer. Salary is commensurate with experience and qualifications.

Qualifications
Successful applicants will hold a Ph.D. or equivalent in a biologically related discipline and will have a track record of developing student-centered learning activities that includes developing course-based undergraduate research experiences or other innovative approaches.

The Department of Biology keenly values diversity amongst its faculty and students and believes it is essential to achieving excellence.

Application Instructions
Applications will be accepted until the position is filled, but to ensure full consideration, complete applications must be submitted by September 30, 2021. To apply, submit a letter of application, a 1-2 page teaching statement, prior research statement, a current curriculum vitae, a copy of an official transcript showing the highest degree conferred (if the Ph.D. is in progress, a copy of the official transcript of completed Ph.D. hours should also be submitted), and names and contact information of 3 individuals that the search committee can contact for letters of recommendation. Inquiries about the position can be sent to Search Committee Chair, Dr. Marcie Moehnke at BioLecturerSearch@baylor.edu.

Posted in: General Message Board → Lecturer in Biology Baylor University

Link to this post \| posted 27 May, 2021 02:10
Tamarah_Adair	debbie Becky, I asked around because I don't use Wine. Tammy Adair (at Baylor) offered this: "As far as I can tell we cannot use wine on any systems past Catalina . Most of my Mac students used a virtual machine set up that our IT department provided. The IT guy that I have been working with for the past 10 years does not see a fix.". This is what I was told- DNAMaster itself is a 32-bit program, as is wine in any stable form (even if there were a stable 64-bit wine it wouldn’t matter as long until/unless DNAMaster goes 64-bit, which is unlikely). The Wine-on-os x method of running DNAMaster on OS X is at an end, as Catalina dropped support for 32-bit apps. If you have a Mac with 10.15 the only option at this point is to run it in a Windows VM (e.g. VMWare).

Link to this post | posted 27 May, 2021 02:10

Tamarah_Adair

debbie
Becky,
I asked around because I don't use Wine.
Tammy Adair (at Baylor) offered this:
"As far as I can tell we cannot use wine on any systems past Catalina . Most of my Mac students used a virtual machine set up that our IT department provided. The IT guy that I have been working with for the past 10 years does not see a fix.".

This is what I was told-
DNAMaster itself is a 32-bit program, as is wine in any stable form (even if there were a stable 64-bit wine it wouldn’t matter as long until/unless DNAMaster goes 64-bit, which is unlikely). The Wine-on-os x method of running DNAMaster on OS X is at an end, as Catalina dropped support for 32-bit apps. If you have a Mac with 10.15 the only option at this point is to run it in a Windows VM (e.g. VMWare).

Posted in: DNA Master → Key Violation

Link to this post \| posted 07 May, 2021 15:10
Tamarah_Adair	I am getting this error, but the link Dan provided is no longer working. Does anyone have an update? Thanks, Tammy

Posted in: DNA Master → SSL error

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