Aromatherapy Research

There is much empirical evidence that exists to support the use of aromatherapy as an accompanying treatment for therapeutic outcomes. In our research study, “Mitigating stress with aromatherapy in individuals with intellectual and developmental disabilities,” Dr. Greenberg and I are whether the use of lavender inhalation will have a notable influence in exonerating stress and restless behavior within a sample of individuals with intellectual and developmental disabilities. Anxiety and anxiety-related disorders are often concomitant with intellectual and developmental disabilities.  The main goals of the study include:

  • To provide this population with a non-pharmacological measure to help meliorate anxiety and stress
  • To provide various disciplines caring for this population with a proactive-instead of reactive-intervention to de-escalate restlessness before a behavioral mediation is necessary

Nursing research and Evidence-based practice (EBP) allows nurses to use scientifically gained evidence for delivering quality health care to a specific population. This research project will help me practice research skills in preparation for advanced practice nursing. I will be responsible for conducting the literature review for best evidence on lavender and stress reduction with individuals (adults) with intellectual disability and writing a systematic review, finding the appropriate measurement scales on stress for the sample, reviewing the IRB application, preparing the study materials, and collecting and analyzing data. To date, Dr. Greenberg and I are currently analyzing scales-tools-measures and deciding on their appropriateness for our sample. When conducting the study, we may use both quantitative and qualitative measures.

Since I have both experience as an RN in working with individuals with intellectual disabilities and contacts in several agencies,  I have also explored the feasibility of conducting the study in three agencies, all serving the population of interest. My next step insofar in agency outreach is to converse with key staff to ascertain the behavioral measures already in use in their facility that are used to measure anxiety, restlessness, and stress.

Once this step is accomplished, we will visit the agencies in order to plan the most appropriate study and data collection.

 

Phenolics in Bee Propolis

Phenolics in Bee Propolis

Research by Josephine Farshi and Professor Elmer Mojica

The primary focus of my Summer 2017 research is the analysis of phenolics in bee propolis. I aim to investigate the properties of this propolis in relation to their use by both bees and humans alike. I will achieve this by studying the antioxidant makeup and nutritional properties of propolis by means of analyzing results gathered from gas-spectrometry mass spectrometry (GC/MS). In this blog post I will describe the purpose of my research, along with how I became interested in the topic.

First, I would like to clarify that bee propolis is a product of bees, but not the commonly presumed product known as honey. The product I am focusing on comes from beehives, just like honey does (Alibino 2014). However, bees make propolis by mixing beeswax with vegetable resin, a brown substance gathered from sap (Castro et al. 2014). Propolis is commonly referred to as bee glue. During the process of GC/MS, the propolis is separated into the chemicals that it consists of during the gas chromatography and further analyzed based on these chemicals during the mass spectrometry overview (Kartal et al. 2002).

Studying the chemical properties, such as flavonoids, will provide insight on how certain chemicals can provide nutritional benefits. The nutritional and food-science aspects behind the bee propolis are what first grabbed my attention about this very topic. For instance, bee propolis is known to contain 300 active compounds, some of which have been used to fight sore throat and stomach ulcers due to the pharmaceutical activities (Rios et al. 2014). I knew that I wanted to work with something related to food-science because I am interested in all aspects of nutrition, including health benefits that certain natural products provide and the effects of socioeconomic status on global nutrient intake. From my research, I aim to see how the chemical composition of bee propolis can be used for benefitting human health.

So far this summer, I have focused on an immense amount of literary exploration. There are several reasons behind why literature is significant in my scientific research. For starters, literature provides me with an understanding of how researchers have previously analyzed the same topic of phenolics in bee propolis. Having a broad understanding of the topic at hand can therefore create a rapport between the audience and myself, as they will be able to trust the authenticity of my studies. By using the Web of Science, I have gathered over 200 abstracts from scientists, published between 2014 and 2017. I now have a broad understanding of the importance of analyzing propolis for both bees and humans alike, along with an established methodology for gathering results.

 

Blog Post #1: The effects of Amyloid Binding dyes on the Cryspovirus in Cryptosporidium Parvum

The purpose of my project is to detect the cryspovirus in Cryptosporidium Parvum. This will be done by cloning GFP, a green fluorescent protein into the virus dsRNA. The GFP gene is inserted into the cryspovirus will make it easier to enumerate the number of virus in Cryptosporidium Parvum.
First I clone out the GFP gene from the pCMV-GFP vector using PCR. I will then extract the PCR product out by the gel extraction technique. From that gel, we will be removing the GFP band containing the restriction sites needed and inserting it into the cryspovirus. To obtain GFP we first need to extract the DNA as well. We will be extracting the DNA from E. coli. The first thing that needs to be done is E.coli with GFP needs to be grown on an agar plate. So the Agar broth and agar were made and Ampicillin was added to both solutions. The agar was poured into an agar plate and left for solidification. Once solidified GFP was streaked onto the plate and left to incubate. The GFP grew very well. Test tubes were made with the agar broth made and tips containing cultures from the E.coli plate. The test tubes have to be incubated while being shaken.  When they grow the liquid will be cloudy. After they grow, QIAprep spin miniprep kit is used to extract the DNA. Once the DNA is extracted it needs to be cleaned by using the DNA clean and concentrator kit. Once our DNA is ready we will PCR it and use it on our gel. We are looking for a specific band and if that band shows up we will remove it from the gel and remove the DNA from the gel. A gel extraction kit is used to remove the DNA. Once the DNA is removed it will be inserted into the cryspovirus dsRNA. I have to extract dsRNA by excystation of Cryptosporidium Parvum oocysts. This breaks the oocysts (shells) that hold the sporozoites. The RNA in the sporozoites is then extracted. The RNA is extracted so we can use PCR to clone in restriction sites. We are currently using different PCR conditions to clone out the different regions of the viral dsRNA.

Blog #1 (07/17/17)

Hello everybody! My name is Ezana Ceman and this is my first blog regarding my summer undergraduate research project with Dr. Parisi. The title of our project is “Estimating Return Periods for Extreme Value Shocks” and we have made really good progress so far. Dr. Parisi was my professor during my first semester of freshman year for CS 113, Mathematical Structures for Computer Science. He was an amazing professor and I enjoyed his class so much! I was so excited when he asked me if I would like to work on a summer research project with him. At first, I was given materials to review regarding how to program using R and what extreme value returns actually are. A majority of our research is being done using R since R is used for statistical modeling so this programming platform is perfect for our work. As of today, Dr. Parisi and I both collectively found the daily, monthly, and annual returns for the four stock market indices we are using; the S&P 500, the Nikkei 225, the FTSE 100, and the Dow Jones Industrial Average. We also found all of the parameters revolving the generalized extreme values (GEV) for all of the stock market indices as well. Dr. Parisi is going to look into all of our data gathered so far to see if there is any seasonality to see if there are any relations there for where the returns spike up or down. Seasonality is a characteristic where you can see if there is any predictability in seeing changes that occur on a yearly basis in a time series. Before our next meeting, I will be gathering data that goes back to the Great Depression as our current data ranges from 1985-May 2017 for the DJIA, 1950-May 2017 for the SPX, 1984-May 2017 for the NIK, and 2009-May 2017 for the FTSE. Having data that goes even further the stock market indices that were around back in the 1920s and 30s will help us have stronger and more concrete return values that will overall help us reach a more valid conclusion. I am looking forward to coming up with a paper for publication with Dr. Parisi and hopefully we find some cool and new interesting commonalities between all of the years and return values so that we can share something new with the world! I attached a few screenshots of some of the plots we have created to go along with our data just to have some visuals within this post and these were all created using R programming!

Quantifying the Number of GFP Expressing Trichomonas Vaginalis Adhering to the Vaginal Epithelial Cells Treated with Amyloid Dyes

Trichomonas vaginalis is a eukaryotic parasite that causes the most common non-viral sexually transmitted infection worldwide. Although it is the most common, it is also the most understudied and poorly comprehended parasite. The research that will be conducted on this organism will help to better understand host-parasite relationship as the trichomonads adhere to vaginal epithelial cells and begin to colonize. The purpose of this research is to successfully quantify the number of GFP expressing Trichomonas vaginalis adhering to the vaginal epithelial cells treated with amyloid dyes. Because there are a lot of trichomonas cells that will be seen under a microscope, the use of GFP or green fluorescent protein will help to magnify and quantify how many cells are present. The goal is to see an increase in fluorescent activity each time the cells are displayed under a microscope.

In order to carryout this research, we first must colonize GFP. To do this, we use GFP that was found in E. coli and smear it onto an agar plate with LB (Luria broth) medium and ampicillin.

(Source: http://microbeonline.com/wp-content/uploads/2016/10/Pour-Plate-and-Spread-Plate-Method.jpg)

Ampicillin is sometimes used on plates because when ampicillin breaks down, it can often lead to more colonies being formed. The plates are then incubated over night to allow for colonization to occur. Once colonization occurs, the plates are moved under a sterile hood and using a sterile pipet and tip, a single colony is extracted and placed into liquid culture made up of the same LB medium with ampicillin and relocated to incubate on a shaker plate over night. The following day, the tubes are removed from incubation and transferred to a microcentrifuge tube and centrifuged out to collect a concise pellet at the bottom of each collection tube. This pellet collected contains bacterial cells that contain GFP, which will eventually be cut out and cloned multiple times. Once the pellet is collected, the DNA is extracted from those cells using a QIA Spin Miniprep kit. The DNA collected after the end of this kit is the unclean DNA, which could possibly contain buffers and residual waste from the kit that was not completely centrifuged out. However, the unclean DNA is tested to make sure that there is indeed DNA present, and to do this, we have to set up a gel electrophoresis.

Gel electrophoresis is a technique used to separate mixtures of DNA, RNA or proteins based on molecular size. Molecules are pushed by an electric field that moves negatively charged particles through the small pores of agarose gel to the positive charge at the other end.

(Source: https://schoolworkhelper.net/gel-electrophoresis-basics-steps/)

Through this technique, we can compare the sizes of bands to a ladder, or just to simply confirm the presence or absence of a specific molecule. For this purpose, we used the gel to determine the presence of bacterial DNA from the E.coli culture. Below is a picture of the resulting gel after running this technique:

As shown by the picture above, DNA was indeed present in the unclean tubes. From those tubes, a certain amount was then collected and another kit, DNA Clean & Concentrator, was used to further clean the DNA to use for a PCR or polymerase chain reaction.

Polymerase chain reaction is used to increase a single copy or a few copies of a section of DNA. Below is a table that shows the main ingredients of a PCR and what their role is:

The main goal to achieve from the PCR is to use the primers that have been specialized to highlight the region used to code for GFP in the DNA sequence, amplify it and cut it out. Once the PCR is complete in the set conditions, another gel is run to determine if the primers worked and if the gene was amplified. However, PCR is a very sensitive technique that requires the right conditions, which have yet to be discovered. Below are the results of the gels following a PCR treatment and the conditions that were set:

1.)

 

2.)

Using these previous conditions, it will allow for us to easily manipulate the numbers to try and find the most ideal conditions. In the future, these ideal conditions will allow for us to isolate the GFP band with the correct restriction sites and insert it into the parasite.

Moving forward, the research aims to successfully obtain the GFP gene in the PCR using the specialized primers. Once this is obtained, we can perform a gel extraction that will isolate the GFP that contains the specific restriction sites that will eventually be cloned and inserted into the parasite in question. As an individual, I hope to perfect my skills in performing a PCR as well as extracting DNA in the form of a pellet. These skills will eventually aid me in my future career as a forensic scientist where the use of PCR is necessary to amplify the DNA in question to perform further tests on it.

Getting Started

I am a junior studying Forensic Sciences.  I knew I wanted to get involved with the undergraduate research program so that I could gain hands-on knowledge about working in the lab.  I am studying breast milk in my summer research.  Human breast milk is important in the health and development of infants, providing crucial nutrients, enzymes, hormones, and antibodies.  It specifically contains proteins, lipids, carbohydrates, and various minerals, all of which are passed to the infant when ingested.  These components vary, however, based on the woman's diet and enviroment before and during lactation.

My research is specifically  analyzing pollutants and toxins in breast milk.  It is well known that pollution in the environment affects many of the products and substances making up food.  Breast milk has a similar solubility to many organic pollutants, so it is not unreasonable to think there are pollutants in breast milk derived products.  The journal "Beverages" ran a special issue on milks, focusing on the bioactive components and its roles in human nutrition.  This opened up the question as to how different pollutants affect both the milk itself, and its roles in human nutrition.

The goal of my research with Dr. Mojica is to not only to analyze the various components of milk products, but to also determine what organic pollutants are present.   I am beginning my research with literature searches, reviewing the studies that have already been done regarding toxins in milk.  From the literature searches, I will narrow down the methods that I will use. After that I will be able to work with Dr. Mojica to decide what methods will be used to determine the various components and narrow down the pollutants to be studied.  After deciding the specific compounds, I will be able to isolate milk samples containing the pollutant in various concentrations and test how the pollutant affects the properties of the milk.  The properties changed in the milk itself will give insight as to how the pollutants can indirectly affect the human nutritional value.

Blog #1

Professor Colman and I’s research is going to focus on how a smoker’s smoking habits effect how long he/she lives. Moreover, we will look at how many much longer a non-smoker or ‘light’ smoker, who smokes once a week, lives versus a ‘heavy’ smoker, who smokes several cigarettes a day. We hope this will help to quantify the exact number of years one’s smoking habits costs them.

We will be using data from the National Center for Health Statistics called the “Public-use Linked Mortality Files” from the years 1986 to 2016. In this data, the sample used is checked every year to see if someone from the sample has died and, if they have, what their cause of death was. We will also be using data from The National Health Interview Survey (IPUMS Health Surveys), which tells us different characteristics of the sample observations (people), such as one’s age, sex, educational attainments, geographical location, marriage status, smoking habits and health statuses. This data will allow us to control for different types of people and how their smoking habits influence how long they live. Right now, we are working on merging these data sets in order to begin our analyses.

The Impact of Cholesterol on Mycobacterium bovis-BCG Resistance to Glutathione

Currently, one-third of the world’s population is infected with Mycobacterium tuberculosis. Of those infections, 10% are characterized by their dormant latent phase and 50% of them are multidrug resistant. As tuberculosis is one of the top ten causes of death throughout the world (World Health Organization), it is pertinent to understand the intracellular response that the human immune response has on M. tuberculosis. When the immune response is activated glutathione (GSH), a thiol based detoxification molecule, is produced to protect the host tissue (Patel et al., 2016). When GSH is secreted it induces uncontrollable reductive stress in the mycobacterial cell, leading to its death.
M. tuberculosis has the ability to enter a latent stage which is characterized by a metabolic shift that allows it to remain dormant inside the host. This is also known as “non replicative persistence,” (NRP). Additionally, being able to hide and remain safe inside the host makes it very difficult to treat. Our research has shown that when BCG is in non replicative persistence, it is resistant to GSH induced reductive stress killing (Patel et al., 2016). Other labs have demonstrated that cholesterol, the sole carbon source for latent Tuberculosis, can be built up inside the mycobacterial cell creating excess NAD+ and NADP that can draw in excess electrons from GSH induced reductive stress (Vandervan et al., 2015). This leads us to hypothesize that the cholesterol induced metabolism will protect M. bovis-BCG from GSH killing similar to how NRP mycobacteria resists GSH. This connection led us to the idea for my project, The Impact of Cholesterol on Mycobacterium bovis-BCG Resistance to Glutathione.
In order to further understand the impact of a cholesterol rich environment, we will be using a NAD/NADH-GloTM Assay. Mycobacterium bovis-BCG will be used as a model organism as it is 99% genetically similar to M. tuberculosis. We expect to see BCG accumulating more NAD+/NADP when it is exposed to the cholesterol. This accumulation would suggest that there was a metabolic shift towards an oxidative environment in the bacterial cytoplasms that is preventing reductive stress killing. This project will further our understanding of the metabolic processes taking place during the infection, and would be beneficial to the development of new vaccinations.

Controlling Tunneling of Heat via Quantum Interference Effects

Our research will examine the quantum processes of heat transfer. Specifically, we will examine these processes as carried by electrons tunneling via the system of coupled quantum dots. We will be using energy-dependent transmission functions and the calculation of quantum heat flux to understand the heat transfer process. Our goal is to develop models in which we can fit experimental data for the purpose of analysis. The analysis will include important conduction mechanisms, operational principles and nanoscale scattering processes.

By working with Dr. Walczak I hope to enhance my understanding of quantum interference by applying models specific to the heat transfer process. In order to be successful in applying such models, I intend to develop a deep understanding of the mathematical aspects of energy transfer processes, including the linear calculation of quantum heat flux and the quadratic correction available by use of Taylor Expansion.

Ultimately, we hope to present our findings at a conference and publish them in a peer-reviewed scientific journal. We believe that the conclusions of this research  will have a significant impact upon our understanding of heat transfer phenomena.

Finding Ways to Manipulate Genetic Information in the Cryspovirus

The purpose of my research project being carried out during Summer 2017 is to find ways to manipulate genetic information in the Cryspovirus. The Cryspovirus is found in Cryptosporidium parvum, which is a parasite. This parasite is known to infect many mammals, birds, and reptiles, and also causes diarrheal disease in humans.

There are many steps that must be taken to be able to manipulate the genetic information of the Cryspovirus. First, RNA must be extracted from the Cryspovirus and then be used to do a polymerase chain reaction, or PCR. Before being able to extract RNA the oocysts, or shells, of Cryptosporidium parvum must be broken so that the Cryspovirus will be accessible and then the RNA can be extracted. With this RNA many PCR’s will be done with different reaction conditions. After the PCR is complete, a gel will be run using primers and the RNA extracted from the Cryspovirus. Polymerase chain reactions of the RNA will continue to be done until a specific band is shown on the gel, which indicates that the PCR worked and that the fragment of RNA extracted from the Cryspovirus was successfully copied.

To be able to see the Cryspovirus in the Cryptosporidium parvum, green fluorescent protein (GFP) gene will be extracted from the plasmid and then cloned and inserted into Cryptosporidium parvum to make the Cryspovirus glow green. To extract the GFP gene, E. coli will be swabbed onto agar plates containing ampicillin and left to grow over night. Once the E. coli has grown, one colony will be picked off of the plate and put into a tube containing agar broth and then left to incubate with shaking overnight until it becomes cloudy indicating growth of the bacteria. After growth has occurred in the tubes, the GFP gene will be extracted using the QIAprep Spin Miniprep Kit and then the extracted DNA will be cleaned using the QIAquick Gel Extraction Kit. The clean DNA will then be used to run a gel with to be sure DNA was extracted. If everything goes as planned then the GFP gene will be cut out of the gel and inserted into Cryptosporidium parvum where it will glow and be easier to see the virus and how it reacts to manipulating its genetic information.