Reminder:
Friday, Oct. 21, 11a.m.-3 p.m.: No heat, hot water, or autoclave capabilities will be available in the FRI Lab.
Showing posts with label Informational. Show all posts
Showing posts with label Informational. Show all posts
Undergraduate Researcher Database
The Council on Undergraduate Research hosts a Registry of
Undergraduate Researchers. The purpose of this registry is to
facilitate matchmaking between undergraduates who have research
experience and a desire to pursue an advanced degree, with graduate
schools seeking high quality students who are well prepared for
research. The Registry is open to students and graduate schools in
the fields of Anthropology/Archaeology, Arts/Humanities,
Biology/Biochemistry, Business, Chemistry/Biochemistry, Economics,
Education, Engineering, English and Linguistics, Environmental
Studies, Geosciences, Health Professions, History, Journalism and
Communications, Mathematics/Computer Science, Physics/ Astronomy,
Political Science, Psychology, Social Work and Sociology.
Any undergraduate may go to https://www.cur.org/ugreg/reg1.asp to fill
out a simple curriculum vitae form. There is no charge to the student
or the student's institution and records will be made available to
bona fide Graduate Schools that contract with CUR for this service.
Organizations or companies seeking the students’ information for other
marketing purposes will not be granted access. Graduate School
representatives may contact students to invite applications or visits
to the campus and laboratory, or to share information about their
research programs and financial support opportunities.
We hope that students who are currently in their junior year will
register now, but anyone with undergraduate research experience may
register at any time. You will be able to update your listing as
appropriate, to include any summer research experience or information
about Senior Theses and test scores. We also welcome submissions by
students who are engaged in Masters' Degree programs now but who plan
on going on to a PhD program. Just fill out the information on the
form including the date you intend to enter a PhD program and your
date of completion of your undergraduate degree. Upload a link to
your CV that contains complete information about your MS/MA degree
activity (school, subject, thesis topic (if applicable), and advisor)
For any further questions contact,
Robin Howard
Senior Director, Membership Services
Council on Undergraduate Research
734 15th St NW Suite 550
Washington, DC 20005
(202) 783-4810x203
(202) 783-4811 fax
Undergraduate Researchers. The purpose of this registry is to
facilitate matchmaking between undergraduates who have research
experience and a desire to pursue an advanced degree, with graduate
schools seeking high quality students who are well prepared for
research. The Registry is open to students and graduate schools in
the fields of Anthropology/Archaeology, Arts/Humanities,
Biology/Biochemistry, Business, Chemistry/Biochemistry, Economics,
Education, Engineering, English and Linguistics, Environmental
Studies, Geosciences, Health Professions, History, Journalism and
Communications, Mathematics/Computer Science, Physics/ Astronomy,
Political Science, Psychology, Social Work and Sociology.
Any undergraduate may go to https://www.cur.org/ugreg/reg1.asp to fill
out a simple curriculum vitae form. There is no charge to the student
or the student's institution and records will be made available to
bona fide Graduate Schools that contract with CUR for this service.
Organizations or companies seeking the students’ information for other
marketing purposes will not be granted access. Graduate School
representatives may contact students to invite applications or visits
to the campus and laboratory, or to share information about their
research programs and financial support opportunities.
We hope that students who are currently in their junior year will
register now, but anyone with undergraduate research experience may
register at any time. You will be able to update your listing as
appropriate, to include any summer research experience or information
about Senior Theses and test scores. We also welcome submissions by
students who are engaged in Masters' Degree programs now but who plan
on going on to a PhD program. Just fill out the information on the
form including the date you intend to enter a PhD program and your
date of completion of your undergraduate degree. Upload a link to
your CV that contains complete information about your MS/MA degree
activity (school, subject, thesis topic (if applicable), and advisor)
For any further questions contact,
Robin Howard
Senior Director, Membership Services
Council on Undergraduate Research
734 15th St NW Suite 550
Washington, DC 20005
(202) 783-4810x203
(202) 783-4811 fax
R0 Pool
For those who needed round 0 pool we are currently out of all round 0 RNA. More RNA can be prepared but it will take about a week to create new pool.
Undergraduate Research Forum
The College of Natural Sciences will host its annual Undergraduate Research Forum on Friday, April 8, 2011 in Welch Hall.
All CNS undergraduate students who have participated in research with CNS faculty or with faculty in other colleges or at other institutions (e.g. summer REU participants) are encouraged to present. The event will feature poster presentations by our top student researchers as well as cash awards for research excellence.
Interested students should first fill out an "Intent to Submit" form on the Student Participants page of the web site above. This connects them to resources and information, including the four workshops we sponsor to help students put together a poster and prepare to present.
Reminder: All undergraduates in the Ellington lab are expected to present their research. This doesn't apply to the freshman who have just entered the stream, but those who work over the summer will be expected to present next spring.
For full list of workshops and more information visit:
http://cns.utexas.edu/research/undergraduate-opportunities/undergraduate-research-forum/workshops
RNA Bead Based Protocol Errors
Target Immobilization: Step 5. Denaturing should be @ 65C instead of 95C.
Eluting and Precipitating the RNA: Step 11. Resuspension should be in 10uL of diH2O not 20uL.
Reverse Transcription: Step 3. This step describes a component of the reaction mixture listed in step 4. I found this confusing when I was first perfroming selections. I think this step should be removed and the RNA template reactant should be added to the Rxn mixture list in step 4.
These are the errors that a few mentors and I knew of. If anyone else finds anything else please add a comment to this post.
(week 10 protocol)
Eluting and Precipitating the RNA: Step 11. Resuspension should be in 10uL of diH2O not 20uL.
Reverse Transcription: Step 3. This step describes a component of the reaction mixture listed in step 4. I found this confusing when I was first perfroming selections. I think this step should be removed and the RNA template reactant should be added to the Rxn mixture list in step 4.
These are the errors that a few mentors and I knew of. If anyone else finds anything else please add a comment to this post.
(week 10 protocol)
TriLink Modified Incorp
If you are considering DNA selections and think modified nucleotides may be of interest, I just got this e-mail from TriLink:
Q - Which of your modified nucleoside triphosphates can be incorporated into DNA molecules through PCR?
A – Aminoallyl-dNTPs, biotin-AA-dNTPs, 2-amino-dATP, 7-deaza-dGTP, and 7-deaza-dATP, 5-Methyl-dCTP, 5-Iodo-dUTP, 5-Bromo-dUTP, 5-Fluoro-dUTP, N4-methyl-dCTP, 5-propynyl-dUTP and 5-propynyl-dCTP, 2-thio-dTTP, 4-thio-dTTP and alpha-thio-dNTPs can be incorporated through PCR. As not all of these analogs will incorporate with similar efficiencies in PCR, some optimization may be needed. We recommend performing some initial PCR experiments using natural:modified dNTPs in ratios such as 1:0, 3:1, 1:1, 1:3 and 0:1 to identify the best conditions for modified nucleotide incorporation with robust amplicon yield.
In addition, 2'OMe-dATP and 2'Fluoro-dCTP can also be incorporated using a modified taq polymerase called Therminator III from NEB. Just ask Mimi. It needs to be optimized, but does work. 2'OMe-dA does not work as well though.
(hint, just click on the image above to see the whole thing)
Methods: A 10cm 10% Native Acrylamide self poured into ready gel housing with long wells was used. 10ul sample + 2ul 5X BioRad dye (Cat # 161-0767) was loaded onto gel. 25 cycles PCR with 45 second steps. 0.1 pmol target.
Observations: 10% Native Acrylamide Gel is easy to pour and takes only 25 minutes to run on these rigs. This gel ran for about 25 minutes at 250V and the darker bromophenyl blue was 1cm from the bottom. The 70bp amplified products midway through the gel with all polymerases tested.
Results: A 70bp product was detectable on the gel for all polymerases with normal nucleotides. However, there were also artifact bands detectable suggesting mispriming or inappropriate cycling conditions. Vent seemed to work the best with the cleanest darkest band for this template using 2’Fluoro dC. Therminator produced artifacts with 2’F dC also. Therminator also produced some smaller termination products with 2’Ome dA seen in lane 3 and 4. Taq polymerase could not incorporate any unnatural nucleotides and also did not show the characteristic banding pattern with natural nucleotides.
Conclusions: The thermo taqs (Therminator, Vent and Vent (-exo) produced banding artifacts with the normal set of nucleotideshese could largely be reduced with modified nucleotide 2’Fluoro-dC. . Therminator, Vent and Vent (-exo) were able to incorporate 2-F dC. None of the polymerases were able to adequately incorporate 2’Ome dA to a sufficient level detectable on this gel. 2’O-Me dA was not a good nucleotide for incorporation enzymatically. For future experiments, use 2’F dC with Vent for incorporation.
Q - Which of your modified nucleoside triphosphates can be incorporated into DNA molecules through PCR?
A – Aminoallyl-dNTPs, biotin-AA-dNTPs, 2-amino-dATP, 7-deaza-dGTP, and 7-deaza-dATP, 5-Methyl-dCTP, 5-Iodo-dUTP, 5-Bromo-dUTP, 5-Fluoro-dUTP, N4-methyl-dCTP, 5-propynyl-dUTP and 5-propynyl-dCTP, 2-thio-dTTP, 4-thio-dTTP and alpha-thio-dNTPs can be incorporated through PCR. As not all of these analogs will incorporate with similar efficiencies in PCR, some optimization may be needed. We recommend performing some initial PCR experiments using natural:modified dNTPs in ratios such as 1:0, 3:1, 1:1, 1:3 and 0:1 to identify the best conditions for modified nucleotide incorporation with robust amplicon yield.
In addition, 2'OMe-dATP and 2'Fluoro-dCTP can also be incorporated using a modified taq polymerase called Therminator III from NEB. Just ask Mimi. It needs to be optimized, but does work. 2'OMe-dA does not work as well though.
(hint, just click on the image above to see the whole thing)
Methods: A 10cm 10% Native Acrylamide self poured into ready gel housing with long wells was used. 10ul sample + 2ul 5X BioRad dye (Cat # 161-0767) was loaded onto gel. 25 cycles PCR with 45 second steps. 0.1 pmol target.
Observations: 10% Native Acrylamide Gel is easy to pour and takes only 25 minutes to run on these rigs. This gel ran for about 25 minutes at 250V and the darker bromophenyl blue was 1cm from the bottom. The 70bp amplified products midway through the gel with all polymerases tested.
Results: A 70bp product was detectable on the gel for all polymerases with normal nucleotides. However, there were also artifact bands detectable suggesting mispriming or inappropriate cycling conditions. Vent seemed to work the best with the cleanest darkest band for this template using 2’Fluoro dC. Therminator produced artifacts with 2’F dC also. Therminator also produced some smaller termination products with 2’Ome dA seen in lane 3 and 4. Taq polymerase could not incorporate any unnatural nucleotides and also did not show the characteristic banding pattern with natural nucleotides.
Conclusions: The thermo taqs (Therminator, Vent and Vent (-exo) produced banding artifacts with the normal set of nucleotideshese could largely be reduced with modified nucleotide 2’Fluoro-dC. . Therminator, Vent and Vent (-exo) were able to incorporate 2-F dC. None of the polymerases were able to adequately incorporate 2’Ome dA to a sufficient level detectable on this gel. 2’O-Me dA was not a good nucleotide for incorporation enzymatically. For future experiments, use 2’F dC with Vent for incorporation.
Notebooks to be Graded
Posted by Alec Rezigh
Hello everyone. I would just like to inform you that I will be collecting the notebooks this week to be graded. This initial grade will be very important to help you develop your "lab notebook" skills and better understand what we are looking for. I will leave comments to help you and feel free to ask any of the mentors, Gwen, or Shawn if you are ever uncertain.
As I work on Saturdays, I ask that all students either leave their notebooks in lab or bring them to me on Saturday by 4 p.m. Your work up to this weeks lab (not including it) will be evaluated. Thanks for your help and comment on this post if you have any questions.
No Pencil In Lab Notebook
I know that some students told me that they wrote all or part of the first lab in pencil. I told them to make sure and write in pen for all future labs and that I didn't think that they had to go back and copy over the pen in ink. I checked with the other mentors, and we do want you to go back and correct your notebooks. I know that it is tedious but these are technically legal documents recording you research. If you dont want to write over it in pen you can also scan it and paste it in you lab notebook.
Sorry about the confusion,
Michael
Sorry about the confusion,
Michael
Snowday Make-up Lecture(s) - Mon. 2/7/11
OK - I had a terrible time trying to write an email with this information. I'm sorry about spamming you early this morning. Here are the details ...
What? Snowday make-up lectures
When? Mon. 2/7/11 at 3:30 and 5:00
Where? **MBB 2.204** (updated at 12:16 pm on 2/7/11)
Who has to go? I strongly recommend that you attend 1 of these lectures, although you are not required to attend. If you're unable to attend 1 of these lectures, then you may email me or Shawn to schedule a meeting to go over the slides.
Slides? The lecture PowerPoint slides are available on Blackboard, like usual.
Questions? Post questions here. :)
See you soon!
Gwen
What? Snowday make-up lectures
When? Mon. 2/7/11 at 3:30 and 5:00
Where? **MBB 2.204** (updated at 12:16 pm on 2/7/11)
Who has to go? I strongly recommend that you attend 1 of these lectures, although you are not required to attend. If you're unable to attend 1 of these lectures, then you may email me or Shawn to schedule a meeting to go over the slides.
Slides? The lecture PowerPoint slides are available on Blackboard, like usual.
Questions? Post questions here. :)
See you soon!
Gwen
Safety Training is Due
Happy (Melted) Snow Day!
The last of your safety training classes is due. Please email Ashley your safety training history. Here's how:
1. Go to this site, https://utdirect.utexas.edu/txclass/index.WBX
2. Log in.
3. Click "Training History" (left side of screen)
4. Make sure you have Adobe Reader on your computer or go to http://get.adobe.com/reader/ to download it for free.
5. On the "Training History" page, go to print & print "Adobe PDF." This prompts you to save the page as a PDF.
6. Email the saved PDF file to Ashley.
Also - the lab will be open tomorrow.
Happy Friday!
Gwen
The last of your safety training classes is due. Please email Ashley your safety training history. Here's how:
1. Go to this site, https://utdirect.utexas.edu/txclass/index.WBX
2. Log in.
3. Click "Training History" (left side of screen)
4. Make sure you have Adobe Reader on your computer or go to http://get.adobe.com/reader/ to download it for free.
5. On the "Training History" page, go to print & print "Adobe PDF." This prompts you to save the page as a PDF.
6. Email the saved PDF file to Ashley.
Also - the lab will be open tomorrow.
Happy Friday!
Gwen
Snow Day?
Are you wishing for snow?
If the weather turns bad, then check this site (http://www.utexas.edu/emergency/index.php) for the status of the University and to see if classes have been canceled. If lecture is canceled, then I'll post the slides on Blackboard (like usual) & we'll stick to the schedule in the syllabus.
Happy Snowmanning/snowballing/iglooing!
Gwen
If the weather turns bad, then check this site (http://www.utexas.edu/emergency/index.php) for the status of the University and to see if classes have been canceled. If lecture is canceled, then I'll post the slides on Blackboard (like usual) & we'll stick to the schedule in the syllabus.
Happy Snowmanning/snowballing/iglooing!
Gwen
1st Quiz of the Semester
Posted by Gwen Stovall
Please complete this online quiz by Sunday, January 30, 2011.
Enjoy!
https://spreadsheets0.google.com/viewform?formkey=dGt4S0pLR05od0VmcmtoMFUwNkp1V3c6MA
Please complete this online quiz by Sunday, January 30, 2011.
Enjoy!
https://spreadsheets0.google.
Welcome Spring 2011 Students to the FRI Aptamer Blog
Posted by Gwen Stovall
Welcome to the Spring 2011 FRI Aptamer Blog. If you are currently enrolled in the class, then you should've received an invitation to write on the blog. Please email me (see syllabus for email address), if you haven't received an invitation.
Please check this site regularly, as we'll regularly post to the site.
Also - please include you name in the posting. This will make it much easier to search for posts by a particular person. For instance, I begin all of my postings with "Posted by Gwen Stovall." Please do the same.
Thank you,
Gwen
Welcome to the Spring 2011 FRI Aptamer Blog. If you are currently enrolled in the class, then you should've received an invitation to write on the blog. Please email me (see syllabus for email address), if you haven't received an invitation.
Please check this site regularly, as we'll regularly post to the site.
Also - please include you name in the posting. This will make it much easier to search for posts by a particular person. For instance, I begin all of my postings with "Posted by Gwen Stovall." Please do the same.
Thank you,
Gwen
Include Name on all Postings
Please include your name in your blog posting. This is necessary to properly search and find blog posts published by a certain person. Although the blog lists the name of the person publishing the post near the title of the post, the website, www.blogger.com, does not allow you to search for all postings by a particular person ... or, I, at least, haven't figured out a way to do this. So - please add your name somewhere in the posting.
Posted by Gwen Stovall
Posted by Gwen Stovall
Pecan Pie Recipe
Hey everyone, here is the pecan pie recipe that everyone loved.
1 (9 inch) pie shell, partially baked – I use the Pillsbury crusts
½ cup butter (1 stick)
1-1/4 cups sugar
½ cup light corn syrup
3 eggs, lightly beaten
1 teaspoon vanilla
1-1/2 cup pecans (whole)
Prepare partially baked pie shell. (Bake for 3 or 4 minutes.) Cook next 3 ingredients (butter, sugar, light corn syrup) over low heat until butter melts. Do not let mixture boil. Cool slightly. Stir in eggs and mix well. Add vanilla and pecans. Pour filling into pie crust. Bake at 375 degrees for 40-45 minutes. Pie should still be soft in the center when removed from oven.
1 (9 inch) pie shell, partially baked – I use the Pillsbury crusts
½ cup butter (1 stick)
1-1/4 cups sugar
½ cup light corn syrup
3 eggs, lightly beaten
1 teaspoon vanilla
1-1/2 cup pecans (whole)
Prepare partially baked pie shell. (Bake for 3 or 4 minutes.) Cook next 3 ingredients (butter, sugar, light corn syrup) over low heat until butter melts. Do not let mixture boil. Cool slightly. Stir in eggs and mix well. Add vanilla and pecans. Pour filling into pie crust. Bake at 375 degrees for 40-45 minutes. Pie should still be soft in the center when removed from oven.
Aliquots and Buffer Needed
We are out of both glycogen and N34 primer(foward and reverse) aliquots. Also, our new 1X TBE buffer for PAGE gels is running very low.
Cheers,
Austin
Cheers,
Austin
End of semester announcements
A few announcements:
1. Happy Thanksgiving!
2. The Lab party will be held during regular lecture time on Tuesday, November 30th at 4:00 in WAG 214. Please sign-up to bring something. Sign-up on the blog.
3. I'll miss the lab party. :( I've enjoyed working with all of you and getting to know you. Please feel free to stop by sometime & tell me how you're blossoming as a scientist. :)
4. Please take the course evaluation/survey. It's available online and Brad may have his own survey as well.
5. Post your lecture presentations on blackboard.
6. Photo slide show - get your lab photos on the stream's Facebook group so we can create a slideshow.
7. Update your resume on friend.cns.utexas.edu, if you haven't already. Remember, the pool of resumes may be used to find scholarship recipients ... free money.
8. Lab clean-up - please perform 2 hours of work in the lab between December 1-3.
9. Final report guidelines are available on Blackboard. The final report is due on December 3rd, because grades are due on Dec 7th. Brad will accept late reports on Dec 5th, minus 15 points. Submit reports on APS blog to your abstract post (like you did with your proposal).
10. Proposals will be graded & returned soon by email.
11. Please read next week's journal article. The article is posted on the APS blog.
Thank you,
Gwen
1. Happy Thanksgiving!
2. The Lab party will be held during regular lecture time on Tuesday, November 30th at 4:00 in WAG 214. Please sign-up to bring something. Sign-up on the blog.
3. I'll miss the lab party. :( I've enjoyed working with all of you and getting to know you. Please feel free to stop by sometime & tell me how you're blossoming as a scientist. :)
4. Please take the course evaluation/survey. It's available online and Brad may have his own survey as well.
5. Post your lecture presentations on blackboard.
6. Photo slide show - get your lab photos on the stream's Facebook group so we can create a slideshow.
7. Update your resume on friend.cns.utexas.edu, if you haven't already. Remember, the pool of resumes may be used to find scholarship recipients ... free money.
8. Lab clean-up - please perform 2 hours of work in the lab between December 1-3.
9. Final report guidelines are available on Blackboard. The final report is due on December 3rd, because grades are due on Dec 7th. Brad will accept late reports on Dec 5th, minus 15 points. Submit reports on APS blog to your abstract post (like you did with your proposal).
10. Proposals will be graded & returned soon by email.
11. Please read next week's journal article. The article is posted on the APS blog.
Thank you,
Gwen
Don't Forget to Access and Submit Course Surveys
The survey period is from November 22 through December 3rd. Don't forget to access and fill these out online. The link should have been e-mailed to you.
SOS PAGE!
Hello everyone! Evidently the lab is out EDTA, thus TBE (we currently lack a lab stock of 10X additionally) and therefore acrylamide cannot be produced!
BlogBooster for iPhone
I just got blog booster free for iPhone and allows me to post here from my iPhone. It's the only free app I've found for blogger. Just letting you know in case you have the need to blog on the go (like I do)
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