Weber State University in Ogden, Utah, is hosting the 2012 National Conference on Undergraduate Research, March 29-31, 2012. Undergraduate students who have participated in research, or other forms of scholarly, creative or artistic work, may submit an abstract to NCUR for possible acceptance and presentation. NCUR will accept abstracts starting October 3, 2011.
Important Abstract Deadlines:
October 3, 2011: Online abstract submission opens
November 15, 2011: Online abstract submission ends and faculty session submission ends
January 6, 2012: Notification of decision on abstracts
For more information, visit weber.edu/ncur2012.
FRI Alumni Contest (Applications due next Monday (10/03))
Are you an Innovator?
The College of Natural Sciences is beginning a new campaign to get the word out about FRI- and the focus is on you-our students and alumni! We'd like to argue that above all, FRI empowers students to do cool things in science- to be real innovators.
We'd like to know your story- how you are an innovator- in your research, as a scholar or as a student. Have you generated a new idea, data no one has ever seen, an image no one has captured before? Are you the first in your family to do research, the first in your hometown? Have you used your college and research experience to take a new direction with your life? To forge a new path?
We want to know. Several students who respond to this call for stories will work with our communication team to further develop a profile as part of our effort to let people know about FRI. This may be a story for the paper, a video, or a web profile. AND the top THREE students will win a $60 gift card to the University Co-op.
If you are interested, please submit a 1-page narrative (it can be lees, but don’t exceed 1 page single spaced) - just tell us your story. This submission won't be published anywhere, so don't stress about it- just let us know how you are an innovator, and we'll follow up with you. Please submit these by Monday, 10/3, via email to (S.L.Simmons@mail.utexas.edu).
The College of Natural Sciences is beginning a new campaign to get the word out about FRI- and the focus is on you-our students and alumni! We'd like to argue that above all, FRI empowers students to do cool things in science- to be real innovators.
We'd like to know your story- how you are an innovator- in your research, as a scholar or as a student. Have you generated a new idea, data no one has ever seen, an image no one has captured before? Are you the first in your family to do research, the first in your hometown? Have you used your college and research experience to take a new direction with your life? To forge a new path?
We want to know. Several students who respond to this call for stories will work with our communication team to further develop a profile as part of our effort to let people know about FRI. This may be a story for the paper, a video, or a web profile. AND the top THREE students will win a $60 gift card to the University Co-op.
If you are interested, please submit a 1-page narrative (it can be lees, but don’t exceed 1 page single spaced) - just tell us your story. This submission won't be published anywhere, so don't stress about it- just let us know how you are an innovator, and we'll follow up with you. Please submit these by Monday, 10/3, via email to (S.L.Simmons@mail.utexas.edu).
Undergraduate Research Funding Opportunity
The Senate of College Councils and the School of Undergraduate Studies invite you to apply for this semester's Undergraduate Research Grant (URG). The URG seeks to encourage students to become actively involved with research in their undergraduate experience providing funding to a deserving applicant. One winner will receive a $1,000 prize from the Senate of College Councils to be used toward funding of his or her research. The grant recipient will be expected to compose a brief paper reflecting on the subsequent research experience at the end of the academic year.
Download the application and get more information here: http://utsenate.org/urg/. Eligible applicants include students assisting a faculty member with a research project, as well as students conducting independent or partnered research. Applicants must be enrolled for 12 hours of coursework at The University of Texas at Austin and be considered an undergraduate students by the UT Office of the Registrar. The deadline for all materials is Friday, November 4th by 5 p.m. Submit your application in person to Becky Carreon in the Senate of College Councils' office, located in SAC 2.102.
Please contact Ryan Hirsch at ryan.hirsch@utexas.edu with any questions regarding the application.
Download the application and get more information here: http://utsenate.org/urg/. Eligible applicants include students assisting a faculty member with a research project, as well as students conducting independent or partnered research. Applicants must be enrolled for 12 hours of coursework at The University of Texas at Austin and be considered an undergraduate students by the UT Office of the Registrar. The deadline for all materials is Friday, November 4th by 5 p.m. Submit your application in person to Becky Carreon in the Senate of College Councils' office, located in SAC 2.102.
Please contact Ryan Hirsch at ryan.hirsch@utexas.edu with any questions regarding the application.
Scholarship Opportunity
Ever wondered about student services on campus?
How are programs designed?
How do administrators make decisions about student life? Why do students act the way they do on campus?
How can you get more from your undergraduate experience?
This could be your lucky day! OUR UT (Opportunities for Undergraduate Research at the University of Texas at Austin), is an undergraduate research initiative sponsored by the Office of the Dean of Students. We are currently accepting applications from all undergraduates to be a part of the program as DoS Scholars.
Students selected to become DoS Scholars will receive $1,000 in scholarship funding over the course of the 2011–2012 school year. OUR UT DoS Scholars are expected to dedicate 3 hours per week to assisting with the Institute's ongoing research projects. Responsibilities may include, reference searching, literature reviews, interviewing, developing surveys, drafting research proposals, designing and pitching research ideas and evaluating programs. In addition, students will learn about research methodologies and practice, as well as the administration of student services under the Office of the Dean of Students.
Our deadline has been extended until this Friday, September 30th.
More information and the application form* can be found on the Dean of Student’s Website or directly at this address: http://deanofstudents.utexas.edu/dri/ourutdosscholarspot/index.php
*It is important to note a CV and letter of reference are required, as part of the application. The reference letter does not have to come from a UT staff or faculty member. We will accept reference letters from other student leaders or representatives of organizations.
How are programs designed?
How do administrators make decisions about student life? Why do students act the way they do on campus?
How can you get more from your undergraduate experience?
This could be your lucky day! OUR UT (Opportunities for Undergraduate Research at the University of Texas at Austin), is an undergraduate research initiative sponsored by the Office of the Dean of Students. We are currently accepting applications from all undergraduates to be a part of the program as DoS Scholars.
Students selected to become DoS Scholars will receive $1,000 in scholarship funding over the course of the 2011–2012 school year. OUR UT DoS Scholars are expected to dedicate 3 hours per week to assisting with the Institute's ongoing research projects. Responsibilities may include, reference searching, literature reviews, interviewing, developing surveys, drafting research proposals, designing and pitching research ideas and evaluating programs. In addition, students will learn about research methodologies and practice, as well as the administration of student services under the Office of the Dean of Students.
Our deadline has been extended until this Friday, September 30th.
More information and the application form* can be found on the Dean of Student’s Website or directly at this address: http://deanofstudents.utexas.edu/dri/ourutdosscholarspot/index.php
*It is important to note a CV and letter of reference are required, as part of the application. The reference letter does not have to come from a UT staff or faculty member. We will accept reference letters from other student leaders or representatives of organizations.
NTC Band
Pool: N58
Everything used were aliquots from the -20 fridge. I'm going to run another NTC using those same tubes, except for the PCR buffer and the reverse primer. I'll post on here when I run the gel and if I get a band.
Tianlu Ma
NTC Band
Posted by: Stephanie Tutak
Hello all,
A band showed up for my no template control (without RNA template) during my Round One of Selection against Tau MAP.
I have the following information about the RNA pool and the reagents used:
RNA Pool: N34
10X PCR Buffer Labeled A-1
EtBr (Personal Aliquot)
dNTP (Row-three, column-six)
N34 Forward and Reverse Primers: Obtained from -20 fridge.
Taq DNA Polymerase: Beta 07/28/11
I used the thermocycler with one block that is on the second bench, but I don't think this is relevant.
Is there anything else that I should mention??
I will be starting this round of selection over again with a different pool of RNA. However, there are only primers for the N34 and N58 pools. If I choose to use a different pool, where should I obtain the proper primers?
Thanks,
Stephanie
Ecology/Integrative Biology Research Opportunity
The project would include collecting and identifying native bees,
identifying native plants, identifying pollen grains with light
microscopy, and determining bumble bee pollen load composition. Other
tasks may include bumble bee DNA extraction and PCR amplification for
population genetics research. For more background on the research
opportunities, undergraduates are encouraged to visit the lab website: Here
Responsibilities include 1) keeping an organized lab notebook, 2)
conducting native plant surveys, 3) collecting and organizing insect
samples, 4) using a light microscope to identify pollen, 5) conducting
DNA extractions, and 6) conducting PCR amplification of microsatellite loci.
Students would start work this semester, and are expected to work for
the next 2-8 semesters.
Students with an interest in Ecology, Evolution, and/or Conservation are
especially encouraged. If interested, please contact the PI via email
at sjha@mail.utexas.edu. In your email, please include 1) related
research work or coursework you have undertaken, 2) your reason for
interest in this project, and 3) hours of availability. If possible,
include a resume/CV.
identifying native plants, identifying pollen grains with light
microscopy, and determining bumble bee pollen load composition. Other
tasks may include bumble bee DNA extraction and PCR amplification for
population genetics research. For more background on the research
opportunities, undergraduates are encouraged to visit the lab website: Here
Responsibilities include 1) keeping an organized lab notebook, 2)
conducting native plant surveys, 3) collecting and organizing insect
samples, 4) using a light microscope to identify pollen, 5) conducting
DNA extractions, and 6) conducting PCR amplification of microsatellite loci.
Students would start work this semester, and are expected to work for
the next 2-8 semesters.
Students with an interest in Ecology, Evolution, and/or Conservation are
especially encouraged. If interested, please contact the PI via email
at sjha@mail.utexas.edu. In your email, please include 1) related
research work or coursework you have undertaken, 2) your reason for
interest in this project, and 3) hours of availability. If possible,
include a resume/CV.
Intramural NIAID Research Opportunities
The INRO program identifies talented students from populations underrepresented in the biomedical sciences who are interested in exploring career opportunities in allergy, immunology, and infectious diseases. INRO 2012 will take place February 6–9, 2012 on the NIH Campus in Bethesda, Maryland.
Applications will be accepted online from August 15 through October 15, 2011.
More information about this program can be found here.
Applications will be accepted online from August 15 through October 15, 2011.
More information about this program can be found here.
Biotinylation of Targets
Hey guys, so I was about to start the selection for my target this semester but realized that it's not a guarantee whether my target (KRAS) is biotinylated or not. This is obviously important because I want to know whether I should perform a bead or filter selection for this target. But this question probably applies to everyone's targets, to what extent should we trust the labeling on the freezer for biotinylated and non-biotinylated?
Thanks,
Ryan
Thanks,
Ryan
Band in CNT
I recently ran a cycle course PCR reaction on 09/15 using the fancy thermocycler on the first bench. a strange band appeared at about 100bp in my NTC lane when i ran the gel of my amplified samples. The picture is a bit blurry:
the lanes on the top left are for wash 3 (cycles 9, 13, 15, and 20). the lanes on the top right are for wash 0 (cycles 9, 13, 15, and 20). the lane on the bottom far left is the NTC and the lanes on the bottom right are for elution 1 (9, 13, 15, and 20). I am well aware that not much appears to be amplified here, which is why i am running another cycle course on my wash 0 and another NTC to see if the band appears again, as its original source is not apparent from the gel.
when running the gel, i used a rig that already had the TBE in it from someone else's previous gel run (no clue who) and im pretty sure it was one of the orange rigs -- although i doubt that matters at all.
From the best of my powers of deductive reasoning, the only specific information on aliquots that i could say for sure is:
-4mM dNTP (2/8/10)
-diH2O (9/7/11 ABR)
-100bp ladder (9/2/11)
-6X orange dye + EtBr (10/27/09 SKP)
none of the 10xPCR buffer or primer aliquots are labeled with dates.
All in all, i won' be sure if this is an actual artifact like Gwen was talking about until i complete my wash 0 and NTC cycle course check, which should be tomorrow sometime.
-Cori Booker
the lanes on the top left are for wash 3 (cycles 9, 13, 15, and 20). the lanes on the top right are for wash 0 (cycles 9, 13, 15, and 20). the lane on the bottom far left is the NTC and the lanes on the bottom right are for elution 1 (9, 13, 15, and 20). I am well aware that not much appears to be amplified here, which is why i am running another cycle course on my wash 0 and another NTC to see if the band appears again, as its original source is not apparent from the gel.when running the gel, i used a rig that already had the TBE in it from someone else's previous gel run (no clue who) and im pretty sure it was one of the orange rigs -- although i doubt that matters at all.
From the best of my powers of deductive reasoning, the only specific information on aliquots that i could say for sure is:
-4mM dNTP (2/8/10)
-diH2O (9/7/11 ABR)
-100bp ladder (9/2/11)
-6X orange dye + EtBr (10/27/09 SKP)
none of the 10xPCR buffer or primer aliquots are labeled with dates.
All in all, i won' be sure if this is an actual artifact like Gwen was talking about until i complete my wash 0 and NTC cycle course check, which should be tomorrow sometime.
-Cori Booker
Dustin Taylor - Link to Proposal
Dustin Taylor
Here's my updated abstract.
Here is a link to my first progress report.
Here's my updated abstract.
Aptamer Selection Against Burkholderia pseudomallei Fimbria Protein for Efficient Diagnosis of Melioidosis
Dustin Taylor – Fall 2011
September 16th, 2011
N58 RNA – B. pseudomallei fimbriae
Burkholderia pseudomallei is a gram negative bacterium that causes the disease melioidosis, marked by the presence of joint pain, cough, skin infections, lung nodules, and pneumonia. It has a niche in soil and surface water, and as a consequence is endemic in Southeast Asian populations where contact with these environments is essentially inevitable.4 It is most commonly acquired through a break in the skin, or by inhaling the aerosolized form of the bacterium.
Most current diagnostics include a complete screening involving numerous cultures and a throat swab; this is very time consuming, and only adds to the 50% mortality rate. Additionally, rapid discovery methods, such as antibody and antigen detection, have relatively low sensitivities averaging around 70%, and as a consequence are not highly trusted.3 The goal of this experiment, then, was to develop an aptamer to more efficiently reveal the presence of a B. pseudomallei infection.
Fimbriae from this particular bacterium have been isolated in order to more easily develop aptamer binders. The specific aim was to select for RNA fragments that demonstrate a high binding affinity for the fimbriae; as this could lead to the eventual development of aptamers for faster diagnostics of the presence of this bacterium in a particular sample.
Figure 1: Illustration of aptamer binding. The specific aim for this selection is to find an aptamer that will bind a bacterial fimbria and provide a quicker diagnostic test for the presence of B. pseudomallei.
The fimbriae proteins have been procured by Kate McCaul of Dr. Kate Brown’s lab. The only remaining step with cost is to functionalize the proteins with biotin. This cost is unknown as the amount of biotin used is target-specific, and has not been recorded.
Here's a link to my proposal.
Here is a link to my first progress report.
Here is a link to my final manuscript.
Nucleic Acid Aptamer Selection Against Myostatin as a Therapeutic Treatment for Amyotrophic Disorders
Santiago Diaz sd24277
Nucleic Acid Aptamer Selection Against Myostatin as a Therapeutic Treatment for Amyotrophic Disorders
The protein myostatin, or GDF8 (growth differentiation factor 8), has been shown to regulate muscle mass growth (myogenesis) by inhibiting myoblast proliferation and differentiation. The theory is that, through a receptor-mediated signal transduction pathway, myostatin stops the cell cycle at G1 phase and prevents myoblasts from undergoing S phase. However, there are people who suffer from muscular dystrophy or other myoatrophic conditions and wish to have greater muscle mass. It is in these scenarios that myostatin inhibition might have beneficial effects.
If the myostatin molecule is somehow disabled or modified so that it can no longer activate the signal transduction pathway, then muscle growth can be promoted. One approach to this task is the use of aptamers, which are RNA or DNA oligonucleotides that are capable of binding to a specific target with high affinity and specificity. Aptamers are designed through a careful process of selection, in which the RNA ligands that bind more strongly to the desired target are replicated. Using these aptamers against myostatin might promote muscle development.
Specific aim 1: Aptamer selection against myostatin protein to inhibit myostatin action.
It is hypothesized that the myostatin aptamers will bind to its target protein before these can reach the receptors that activate the signal transduction pathway that negatively regulate proliferation and differentiation. The myostatin-aptamer conjugated protein will have such a foreign shape and form that, when it reaches the receptor, the binding site will not recognize it, rendering it incapable of triggering the signal transduction pathway, and thus, unable to inhibit muscle growth. The aptamer could also act as an allosteric inhibitor, by binding to the receptor binding site and inhibiting myostatin action.
Figure 1. Diagram of the development of myotubes(muscle cells). The black lines show at which points in the process does myostatin (MSTN) exert its negative regulation. The red lines show where the aptamers will take action to prevent myostatin from triggering the signal transduction pathway. Picture courtesy of Rios, Ramon (2001).
Myostatin can be obtained from Shenandoah Biotechnology, Inc. for $165 per 10 ug. The catalog number is 100-22.
Sources:
Rios, Ramon (2001) "Myostatin is an inhibitor of myogenic differentiation" American Journal of Physiology: Cell Physiology.
Thomas, Mark (2001) "Myostatin, a Negative Regulator of Muscle Growth, Functions by Inhibiting Myoblast Proliferation" The Journal of Biological Chemistry.
Whittemore, Lisa-Anne (2003) "Inhibition of myostatin in adult mice increases skeletal muscle mass and strength" Biochemical and Biophysical Research Communications. Volume 300, Issue 4, Pages 965-971
See the whole proposal
To see my progress report 1, click here.
To see my final manuscript, click here
Subscribe to:
Posts (Atom)