Matching Items (19)

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A Hands-On Activity to Demonstrate the Central Dogma of Molecular Biology Via a Simulated VDJ Recombination Activity

Description

Essential or enduring understandings are often defined as the underlying core concepts or “big ideas” we’d like our students to remember when much of the course content has been forgotten.

Essential or enduring understandings are often defined as the underlying core concepts or “big ideas” we’d like our students to remember when much of the course content has been forgotten. The central dogma of molecular biology and how cellular information is stored, used, and conveyed is one of the essential understandings students should retain after a course or unit in molecular biology or genetics. An additional enduring understanding is the relationships between DNA sequence, RNA sequence, mRNA production and processing, and the resulting polypeptide/protein product. A final big idea in molecular biology is the relationship between DNA mutation and polypeptide change. To engage students in these essential understandings in a Genetics course, I have developed a hands-on activity to simulate VDJ recombination. Students use a foldable type activity to splice out regions of a mock kappa light chain gene to generate a DNA sequence for transcription and translation. Students fold the activity several different times in multiple ways to “recombine” and generate several different DNA sequences. They then are asked to construct the corresponding mRNA and polypeptide sequence of each “recombined” DNA sequence and reflect on the products in a write-to-learn activity.

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Created

Date Created
  • 2017-08-11

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Analysis of differential secondary effects of novel rexinoids: select rexinoid X receptor ligands demonstrate differentiated side effect profiles

Description

In order to determine the feasibility of utilizing novel rexinoids for chemotherapeutics and as potential treatments for neurological conditions, we undertook an assessment of the side effect profile of select

In order to determine the feasibility of utilizing novel rexinoids for chemotherapeutics and as potential treatments for neurological conditions, we undertook an assessment of the side effect profile of select rexinoid X receptor (RXR) analogs that we reported previously. We assessed pharmacokinetic profiles, lipid and thyroid-stimulating hormone (TSH) levels in rats, and cell culture activity of rexinoids in sterol regulatory element-binding protein (SREBP) induction and thyroid hormone inhibition assays. We also performed RNA sequencing of the brain tissues of rats that had been dosed with the compounds. We show here for the first time that potent rexinoid activity can be uncoupled from drastic lipid changes and thyroid axis variations, and we propose that rexinoids can be developed with improved side effect profiles than the parent compound, bexarotene (1).

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Agent

Created

Date Created
  • 2015-03-16

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Integrating Ethics into Case Study Assignments

Description

I teach an upper-level writing course, Genes, Race, Gender, and Society, designed for Life Science majors, in which I utilize a case study to expose students to ethical ways of

I teach an upper-level writing course, Genes, Race, Gender, and Society, designed for Life Science majors, in which I utilize a case study to expose students to ethical ways of thinking. Students first work through the topical case study and then are challenged to rethink their responses through the lenses of ethics, taking into account different ethical frameworks. Students then develop their own case study, integrating ethical components. I want to expose my students to this way of thinking because I see technology being driven by the Jurassic Park phenomenon, “Your scientists were so preoccupied with whether or not they could, they didn’t stop to think if they should,” and want future physicians grounded in a sense of how their actions relate to the greater good.

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Created

Date Created
  • 2014-12

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From Pipe Cleaners and Pony Beads to Apps and 3D Glasses: Teaching Protein Structure

Description

Students often self-identify as visual learners and prefer to engage with a topic in an active, hands-on way. Indeed, much research has shown that students who actively engage with the

Students often self-identify as visual learners and prefer to engage with a topic in an active, hands-on way. Indeed, much research has shown that students who actively engage with the material and are engrossed in the topics retain concepts better than students who are passive receivers of information. However, much of learning life science concepts is still driven by books and static pictures. One concept students have a hard time grasping is how a linear chain of amino acids folds to becomes a 3D protein structure. Adding three dimensional activities to the topic of protein structure and function should allow for a deeper understanding of the primary, secondary, tertiary, and quaternary structure of proteins and how proteins function in a cell. Here, I review protein folding activities and describe using Apps and 3D visualization to enhance student understanding of protein structure.

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Created

Date Created
  • 2014-12

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Treatment for T-Cell Lymphoma Cancer: Synthesis of Analog Compound of Bexarotene

Description

Cancer, a disease which affects many lives, has been the topic of interest for this research. Treatment options are often available to help lessen the effects of the disease and

Cancer, a disease which affects many lives, has been the topic of interest for this research. Treatment options are often available to help lessen the effects of the disease and in regards to cutaneous T-cell lymphoma (CTCL), no cure currently exists. An FDA approved drug by the name of Bexarotene has been developed to provide chemotherapeutic effects within CTCL. Bexarotene has also been used in trials of breast cancer, lung cancer, glioblastoma multiforme and various neurodegenerative diseases. Yet the medication often causes serious side effects including hyperthyroidism, raised triglyceride levels and cutaneous toxicity. The focus of this research is to synthesize a hydroxylated analog compound of Bexarotene in efforts to produce a molecule that provides better chemotherapeutic effects while also lessening the various side effects caused. Synthesis of the molecule followed various organic chemistry techniques and reactions to create the final product. Melting point analysis, NMR and other various characterization data helped to confirm the synthesis of the intended molecule. Preliminary bioassay data results of the analog compound showed similar potency to that of Bexarotene. Further testing, however, will be required to determine the full pharmacokinetic profile of the molecule. Future direction of the research focuses on both further testing of the hydroxylated analog as well synthesizing newer analog compounds to find a molecule that can provide the best effects within cutaneous T-cell lymphoma and the various other diseases as well.

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Created

Date Created
  • 2018-05

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The Effects of Ferulic Acid Concentration on Yeast DNA Repair After Exposure to UV Radiation

Description

Exposure of harmful ultraviolet rays (UV) is a great concern in many locations around the world, as skin diseases and cancer continue to surge. With the number of skin cancer

Exposure of harmful ultraviolet rays (UV) is a great concern in many locations around the world, as skin diseases and cancer continue to surge. With the number of skin cancer skyrocketing past all the types of known cancers, a vast majority of cases are reported daily. When the skin is exposed to UVA or UVB radiation, primarily from the sun, the UV radiation damages the DNA within the cells, which results in skin cancer. However, most damaged DNA of cells can undergo nucleotide excision repair. This involves a nuclease molecule that cuts the damaged bases. Preliminary research has developed other ways of repairing DNA damage in cells by implementing organic compounds. An organic chemical such as, ferulic acid has the ability to aid the mechanisms involved in nucleotide excision repair that takes place in your cells after DNA damage.

To test this, Saccharomyces cerevisiae was utilized. This is a primary model used in most medicinal studies due to the resemblance to human cells. This study evaluates the effect of ferulic acid, concentrations on ultraviolet radiated Rad 1 (mutant) and HB0 (wild type) yeast cells. The yeast strains were grown in two different concentrations for ferulic acid and treated with long-wave UV light under 30 seconds, 45 seconds, and 60 seconds. It is observed that, Rad 1 had heavier growth in the presence of high concentration of ferulic acid after UV treatment than HB0. But, HB0 yeast had heavier growth in the presence of lower concentrations of ferulic acid after UV treatment. Ferulic acid concentrations of 1 mM can influence cell repair after UV application by mRNA expression during nucleotide excision repair and higher absorption of UV.

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Created

Date Created
  • 2020-12

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Oral Microbiome Analysis Reveals Potential for Streamlining Diagnosis of Rheumatoid Arthritis

Description

Rheumatoid Arthritis (RA) is an autoimmune disorder where the body mistakenly attacks healthy joints. This in turn causes inflammation resulting in pain and swelling. It is very important to get

Rheumatoid Arthritis (RA) is an autoimmune disorder where the body mistakenly attacks healthy joints. This in turn causes inflammation resulting in pain and swelling. It is very important to get RA accurately diagnosed and treated as early as possible. Similarly, with any disease: the longer it is left untreated, the more damage it can cause. RA can cause irreversible joint damage leading to disability. The purpose of this study is to determine if oral microbiome can be used as an additional criterion to aid in diagnosing RA. Several oral microbes have already been identified as biomarkers for RA in saliva. In this study, 10 participants were recruited: 6 diagnosed with RA and 4 Healthy as a control. Two subgroups of RA were done within this study; those diagnose with a positive Rheumatoid Factor (RF) and those diagnose with a negative RF. These subgroups were then compared in order to determine the validity of using certain microbes as biomarkers for RA even when different diagnostic criteria were met. The microbe Parahaemolyticus had the largest measure of effect, showing the greatest potential for statistically significant results with a larger sample size. If we can work narrow to down specific microbes to be undoubtedly higher in abundance with already diagnosed RA patients when comparing to healthy participants, this will be a gamechanger. Not only could we give a higher sense of confidence with the diagnosis of RA, but this could streamline RA diagnosis.

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Created

Date Created
  • 2020-12

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Promoting Scientific Literacy in High Schools

Description

Scientific literacy is a critical part of the education of high school students. Students can demonstrate literacy in science by being able to read and write scientific reports as well

Scientific literacy is a critical part of the education of high school students. Students can demonstrate literacy in science by being able to read and write scientific reports as well as recognize and discuss how science affects daily lives. However, many teachers are not familiar with the topic and do not have the resources necessary to implement it into their classrooms. This project attempts to create a website that compiles information from many sources to one concise location that is simple for teachers to use. The goal of the website is to provide teachers with a resource that they can access and use quickly despite their busy schedules. The information provided is easily translatable into a classroom, and examples of lessons as well as links to resources are provided. Considerations of difficulties such as the need to prepare students for standardized tests as well as limited budgets were brought into consideration when choosing the concepts suggested for teachers. Aspects of scientific literacy addressed are: project based learning, virtual labs, apprenticeship programs, and peer mediated learning strategies. The project also addresses how demographics that are represented at lower levels in science can be aided. These groups include female students, minorities, and students with High Functioning Autism (HFA). The website portion of the project is accompanied by a paper that summarizes the research findings as well as the personal reaction of the author and how her teaching has been affected by the study. Upon completion of the project the website will be shared with school districts across Phoenix to provide teachers with access to the resources compiled in it.

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Agent

Created

Date Created
  • 2015-12

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Luminometric Analysis of Yeast Calcium Channel Homeostasis Following Hypotonic Shock

Description

Calcium is the only ion capable of triggering electrical and chemical reactions in cells which are part of essential biomolecular processes, such as gene transcription and ion flux. Calcium homeostasis,

Calcium is the only ion capable of triggering electrical and chemical reactions in cells which are part of essential biomolecular processes, such as gene transcription and ion flux. Calcium homeostasis, the control of concentration levels, is therefore crucial for the proper functioning of cells. For example, cardiomyocytes, the cells that form cardiac muscle, rely on calcium transfer process to produce muscle contraction.
The purpose of this work is to study aspects of calcium homeostasis in the model organism Saccharomyces cerevisiae, common yeast. Using luminometric techniques, the response of the yeast was monitored against a set of changes in the environment calcium abundance. The results indicate a complex response as both increase and decreases of external calcium induce elevations in cytosolic calcium concentrations.
Calcium is transferred across compartments by means of channels. In Saccharomyces cerevisiae, many of them have been identified; Cch1p-Mid1p, Vcx1p, Pmc1p, Pmr1p, and Yvc1p. Their participation in calcium homeostasis is well established. Observations of cytosolic calcium increase after a hypertonic shock are mainly associated with influx of ions from the environment though the Cch1p-Mid1p. This process is generally considered as driven by calcium concentration gradients. However, recent studies have suggested that the plasma membrane channel, Cch1p-Mid1p, may possess more sophisticated regulation and sensory mechanisms. The results of our experiments support these ideas.
We carried out experiments that subjected yeast to multiple shocks: a hypertonic shock followed by either a second hypertonic shock, a hypotonic shock, or a yeast dilution pulse where the solution volume increases by the calcium concentration has only a small change. The cytosolic calcium concentration of a yeast population was monitored via luminometry.
The main result of this study is the observation of an unexpected response to the combination of hypertonic and hypotonic shocks. In this case it was observed that the cytosolic calcium concentration increased after both shocks. This indicates that cytosolic calcium increases are not solely driven by the presence of concentration gradients. The response after the hypotonic pulse arises from more complex mechanisms that may include sensor activity at the membrane channels and the release of calcium from internal storages.

Contributors

Agent

Created

Date Created
  • 2020-05

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Luminometric Analysis of Yeast Calcium Channel Homeostasis Following Hypotonic Shock

Description

Calcium is the only ion capable of triggering electrical and chemical reactions in cells which are part of essential biomolecular processes, such as gene transcription and ion flux. Calcium homeostasis,

Calcium is the only ion capable of triggering electrical and chemical reactions in cells which are part of essential biomolecular processes, such as gene transcription and ion flux. Calcium homeostasis, the control of concentration levels, is therefore crucial for the proper functioning of cells. For example, cardiomyocytes, the cells that form cardiac muscle, rely on calcium transfer process to produce muscle contraction.
The purpose of this work is to study aspects of calcium homeostasis in the model organism Saccharomyces cerevisiae, common yeast. Using luminometric techniques, the response of the yeast was monitored against a set of changes in the environment calcium abundance. The results indicate a complex response as both increase and decreases of external calcium induce elevations in cytosolic calcium concentrations.
Calcium is transferred across compartments by means of channels. In Saccharomyces cerevisiae, many of them have been identified; Cch1p-Mid1p, Vcx1p, Pmc1p, Pmr1p, and Yvc1p. Their participation in calcium homeostasis is well established. Observations of cytosolic calcium increase after a hypertonic shock are mainly associated with influx of ions from the environment though the Cch1p-Mid1p. This process is generally considered as driven by calcium concentration gradients. However, recent studies have suggested that the plasma membrane channel, Cch1p-Mid1p, may possess more sophisticated regulation and sensory mechanisms. The results of our experiments support these ideas.
We carried out experiments that subjected yeast to multiple shocks: a hypertonic shock followed by either a second hypertonic shock, a hypotonic shock, or a yeast dilution pulse where the solution volume increases by the calcium concentration has only a small change. The cytosolic calcium concentration of a yeast population was monitored via luminometry.
The main result of this study is the observation of an unexpected response to the combination of hypertonic and hypotonic shocks. In this case it was observed that the cytosolic calcium concentration increased after both shocks. This indicates that cytosolic calcium increases are not solely driven by the presence of concentration gradients. The response after the hypotonic pulse arises from more complex mechanisms that may include sensor activity at the membrane channels and the release of calcium from internal storages.

Contributors

Agent

Created

Date Created
  • 2020-05