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Class Projects


Biology Working Group, Project List, 2/2/2012

 Several students have proposed projects related to biology. All of these projects are collected here.

 Paul Szauter 2/2/2012
2. Open-Source Agriculture. The techniques of crop improvement, including genome analysis and genetic modification, have yet to be fully applied to improving indigenous crops in the developing world. The aim of this project is to identify food crops that would be good targets for improvement in a model where the work is sponsored by a public agency or foundation rather than by a corporation. The project might include open-source collaboration and challenge awards, approaches borrowed from collaborative software development and other crowdsourcing models.

Please see also World Hunger, posted 2/5/2012.

3. Colony Collapse Disorder. Domesticated honeybees are essential to pollinate many agricultural crops. Colony Collapse Disorder is a complex disorder that causes the loss of entire hives. The aim of this project is to develop improved strategies to monitor, understand, and prevent Colony Collapse Disorder.
4. Improve Sample Prep for Ion Torrent Sequencing. Ion Torrent sequencing is a massively parallel sequencing strategy based on integrated circuit technology. Sample preparation requires approximately eight hours. The aim of this project is to develop techniques to reduce the sample preparation time to four hours or less. This project is a current challenge from Innocentive.
12. Simplified Lab Techniques. Many routine laboratory techniques are not as foolproof as they could be. The aim of this project is to increase the reliability of laboratory techniques through simplification and standardization, without regard to cost.

 Sarah Kintner 2/4/2012
4. Algae Metagenomics (Graduate Project). Use pyrosequencing to characterize New Mexican algae communities seeking the best candidate for algae biofuel production. The development of a workable testing matrix using (2-3) communities plied against (3-4) culling challenges (i.e. high light intensity, high temperature, high salinity and cold temperature) with the expected result that the survivor(s) would be the best candidate(s).

 Anna Bancroft 1/30/2012
1. How can we reduce obesity? Could something like a portable insulin level monitor help?
3. Learning and Pregnancy. What prompts the swift increase in learning capacity (synapse formation) during pregnancy and shortly thereafter? Do similar effects occur on BCPs? Could the biological conditions be created at other times/ for men?
7. Low Gravity. What could low gravity do for medical treatments?

 Regina Rendon 1/29/2012
2. Transcranial Direct Current Stimulation and its clinical effects. The goal of this project it to see how tDCS can be used to determine the biological basis of memory processes, drug addiction, depression and other clinical issues.

 Olivia Pena 1/30/2012
3. Antibiotic replacement. Find some other type of antibacterial agent than current antibiotics to be used after birth. This will help prevent such diseases as asthma and allergies that occur as a result of antibiotic use.
7. Migrane Treatment. Migrane sufferers have no treatment. This will help find treatment for migrane sufferers by study of LSD and possible analogues without addictive or hallucinatory qualities.

 Terrill Yazzie 1/30/2012
4. Save the ocean. It is believed that water perpetuates life. The Ocean is a vast ecosystem that must be protected. The aim of this project is to protect the ocean by developing ways of improving the primary productivity of the organisms by identifying the real picture of what bacteria are really there.
5. Keystone Species Keystone species play an important role in ecosystems. The aim of this project is to develop models that help in identifying which animals are considered keystone in their habitat to help identify which ecosystem could potentially be threatened if they are absent.
6. Biofuels. Tumbleweeds grow profusely around the desert. They are easily maintained and require very little water to produce robust biomass. The aim of this study would look at each species of weeds and determine which type would be suitable for biofuel generation.
8. Bacteria Identification Many culturing techniques are bias by not identifying the true bacterial population that they do not allow certain organisms to grow. The aim of this project is to develop new ways to culture and grow microbes that allow for true identification rather than through genetic tests that are costly and time consuming.
10. Food shortages. The foods that we eat are becoming scarce due to changes in the earth's composition. The aim for this project would be to investigate indigenous foods, such as eating insects (whose population is numerous), to explore new ways to nurture a starving world.

 Jennifer Piarowski 1/30/2012
2. Species Database. world-wide internet database with species identification information and capabilities

 Jeremiah Anderson 2/6/2012
1. Better Rubisco. Rubisco has low CO2 specificity, often uses O2, and is slow. This leads to much of the plants resources going to make lots of Rubisco. A faster, more specific enzyme would be ideal as there would be more resources for the plant to make other things.
3. New PTSD/TBI therapies. Post traumatic stress disorder and traumatic brain injury have usually been separate. However, with improvised explosive devices, service men and women are usually coming home with both requiring new therapies to deal with problems that arise from both. And let's face it, Marines don't like talking out their feelings and experiences with outsiders.

 Marie Reyes 1/30/2012


The purpose of this project is to find a way to test for the presence of an allele which serves as a marker for predisposition to develop Post Traumatic Stress Disorder (PTSD). This allele is present in many adults, some are homozygous for the trait and others are heterozygous. They will be herein referred to as the Long or Short allele. Studies have correlated the presence of the short allele with a predisposition to develop PTSD. Since PTSD is a complex human behavioral disorder, of which the entire etiology is not known, the presence of this allele represents only a small piece of information in a highly complex web of neurobiological function.

The development of this test is crucial in preventing onset of the disease by reducing exposure to traumatic events like combat for example. Genetic testing is expensive and a more cost effective way to detect vulnerability is needed. A test that requires minimal training to perform and with materials that are cost-effective. So far, we have been able to repeat previous experiments to amplify by PCR the sequence of variance (Mellman et al. 1996, Gerlerntner et al. 1993). This has been done by taking blood samples from donor volunteers. We used the GC rich from Roche along with the Taq PCR all in one tube and imaged using etBR (ah! I'll put the detail of kits in the final paper) We can use PCR and gel electrophoresis as a way to test our results we get with the new method. What is the most cost effective, simple way to test for allelic variation?

In order to improve upon previous work, we plan to use a less invasive approach to scan DNA samples: Urinalysis. There is a kit from Qiagen which claims to extract an average 25ug of DNA from urine samples. We can first utilize this kit and later develop our own protocol to quickly extract DNA from urine samples. Due to the 44bp deletion in the short version of the allele, we will use a generated probe that will hybridize to the region of interest located in the long allele. The probe should be designed in a way that it can recognize the sequence, incubation/hybridization period is short and visualization of the results can be seen without the use of special equipment or machines. The probe hybridization presents the biggest challenge in this project. Is there a way to develop the probe so that it can hybridize quickly and consistently? Southern blotting by way of random-oligo-primed-synthesis is a widespread method used to probe for specific sequences. Although this is typically used in conjunction with Polymerase Chain Reaction using expensive enzymes.

Is there a way to bypass this part of the process? Can we utilize other ideas in molecular biology to solve this problem? Often, people use immunohistochemistry (want to expand on this idea) to detect the presence of certain compounds expressed in the cell. This is the case in Western Blotting but often we are detecting using antibodies, but can a similar approach be used for our purpose? Approaches using liposomes to detect hybridization have been used frequently in immunology studies, perhaps there is a way to expand on those ideas. In designing the probe, I would like to combine a variety of approaches to be able to detect hybridization of the probe and then visualize the results. Paper chromatography, as used in the fields of chemistry as well as molecular biology is useful for quick visualization to detect the presence of a molecule/compound using reactive dyes that simply use nitrocellulose paper along with chemical tagging to produce a visual reaction (Zhang et al. 2000, Rule et al. 1996). Using a known genotype positive for the long allele as a control, we should conduct testing simultaneously using the probe and paper chromatograph. We can quantify our results by using a method similar to statistical analysis of Western Blotting. If the allele is present, there should be two positive reactions indicated by color change and if the allele is not present, one positive (control) and one negative reaction.

In development

Rule et Al. 1996
Gerlerntner 1993
Mellman 1996
Zhang et Al. 2000

 Amber Leigh Ortiz 1/29/2012
Current Lab Work: Project 1

Can mNPs be endocytosed in Breast Cancer cells as a Cancer Therapy Using an AMF to cause hyperthermia?

  • Will the cell take up the mNPs?
    • What surface characteristic will increase the possibility of endocytosis?
  • Can the cells be killed by heat?
    • What temperature?
    • How long?
  • Will the AMF increase the residual heat with the help of the mNPs?
  • How are the mNPs taken up by the cells?
    • Endosomes
      • Test using EEA1 antibody
    • Lysosomes
      • Test using LysoTracker
  • Do the mNPs have any inherent toxicity?
    • At what concentrations?
    • Time?
  • How long must the cells incubate with the mNPs?
    • What happened overtime?
    • 30min --> 24hrs
  • Will targeting be used?
    • If not why?
    • How? What can/will be used?

Future Directions:

  • Clinical, how will treatment be applied?