A Little Piece of Advice

Before I transferred to ASU, I made sure I was taking classes I needed for my major and research certificate. While at Phoenix College, I had the idea that a research certificate was required for the TRAIN scholarship. So, with that in mind, I had talked to an advisor and everything seemed to check out. I was taking Genetics, Statistics, Sign Language and IAS (a required transfer class). I thought I was on the right track but that changed half way into the semester. It was Halloween and this was the last day to withdraw from any class. I was doing horrible in Statistics (below passing horrible). I went to every class and took notes but that was a class where I understood in class but as soon as I walked out or took a test, I forgot everything. That class was not it but I had to take it for my scholarship (or so I thought). That day, I had to consider whether I should withdraw and take it next year or continue with it (which would have been a dread). I didn’t know what to do so I reached out to Dr. Hackney Price and Dr. Marshall. After explaining my situation, they gave me advice and I decided to withdraw from the class. I also learned that the research certificate was NOT required for the scholarship (hallelujah)! Moral of the story: don’t be afraid to quadruple check your work with various and different people, even if you think you’re done. It might seem annoying or repetitive but hey, this is your education. I thought I had my classes in check but it turns out I didn’t. If I could go back and change that, I would. I wasted my time on a class I didn’t need and I could’ve used that time for a class I would’ve enjoyed. Also, don’t be afraid to ask for advice. Faculty is there to help YOU! At the end of the day, they are more knowledgeable and experienced so asking them doesn’t hurt you or them. All in all, I will definitely continue to use this advice and I hope it was helpful!

Figure 1. My reaction when I found out I could've saved myself the stress, Friday night homework and a 1-hour class 3 times a week ("Are you kidding me Template", n.d.). Save yourself from this disappointment and follow my advice, please.

Citation
Are you kidding me Template. (n.d.). Retrieved from https://imgflip.com/memetemplate/64537068/Are-you-kidding-me

Interview with Dr. Jennifer Hackney Price

This semester, as some may know, I have been interning in Dr. Jennifer Hackney

Price’s lab. Even though research has been slow (our virgin flies died after

collecting them for 2 weeks), I have learned how to identify flies and the

genetics behind the project. Dr. Hackney Price is an amazing mentor and I truly

cannot express how happy I am to be in her lab. With this in mind, I interviewed

her to see what her job was like.

Me: What is the best thing you like about being a professor?

Jennifer Hackney Price: Interacting with the students. It’s been fun to do
interactions with them in a lab, which I get geeked out about anyways,
because folks bring such good energy and interesting ideas.

Me: Is it because you like helping or the personalities? What about the
students makes it fun?

Hackney Price: I think a little bit of both. Probably more of the
personalities because undergraduates come in with new ideas and they
haven’t been exposed to different techniques and fields. Everything they
come with is so brand new. Especially in lab, you guys come into lab
with all these crazy ideas and it’s like ‘wow, I never would’ve thought of
that! Let’s do it and see what happens!’, which is fun. In the classroom,
seeing the A-HA moments when it finally clicks and I’m just like ‘YES!’.

Me: [laughs] That’s nice, so what about the worst?

Hackney Price: [exhales] Can I say the same answer? [Laughs] As
excited as I get working with undergrads, you guys can be the most
frustrating group of people to work with. There’s been times when I’m
teaching and I see students that I know can do such a great job and then
they won’t show up to class, aren’t taking notes or don’t do the work. It
drives me absolutely batty because I know they can pass the class with
flying colors. I wouldn’t say it’s the worst thing but it is frustrating. The
other part is the flip side. There are students who pour their heart into
classes, show up to office hours, I teach them in a number of different
ways and encourage them but if it doesn’t click, there’s nothing you can
do. That’s a tough pill to swallow.

Me: A disappointment for sure. Why did you decide to enter your field?

Hackney Price: I’ve always loved science. I’ve always been a lab rat.
I’ve always been the science nerd. I remember, as a kid, I had a rock
collection and every rock was amazing. I’d show my parents my rocks
and they were so annoyed with me, carrying around my pocket-loads of
rocks. It’s always kind of has been who I was, I always wanted to figure
out what’s going on, how stuff works. I suppose it was in my genes.

Me: I was about to say that it was in your DNA [laughs]. With that,
what is the most surprising thing about your field, to you?

Hackney Price: How open the scientific community is. I’ve had so
many people share information with me that wasn’t published. People
are willing to share information, supplies and reagents to help move the
field along. That kind of sense of community is something I never even
thought about. For developmental biology, I have found that everybody is
helping each other out.

Me: That’s interesting to know because I thought the scientific community
would be competitive like ‘who’s going to do the next big thing?’ or
‘who’s going to cure cancer?’.

Hackney Price: Don’t get me wrong, some fields are more competitive
than others. In the fly community, there are a few notorious labs that are
really hard to work with. There’s a lot of variation but just in general,
I think folks who got into science did it because they want to know what’s
going on and the only way to do that is to work with each other.

Through this interview, I found out more about her and the way she thinks. I
hope some of you were able to capture her honesty and humor. Until next time!

Figure 1. The developmental process of Drosophila melanogaster a.k.a fruit fly ("Invertebrate development: Drosophila", n.d.). Dr. Hackney Price's lab studies the genetics of these flies to better understand human genetics (the genes of these flies are closely related to those of humans).

Citations:
Invertebrate development: Drosophila. (n.d.). Retrieved October 27, 2018, from Overview of development website: http://biology.kenyon.edu/courses/biol114/Chap12/Chapter_12b.html

Feeling Comfortable

I don’t usually drink coffee but I wanted to try a new drink from Starbucks. I ordered a tall (aka short) Cacao Protein Blended Cold Brew. It sounded fancy and good so I didn’t see a reason why not to order it… until the barista looked at me confused. He asked me, “are you sure you want that one?” After explaining to him that I usually go for sweet drinks, he told me that I probably won't like it. However, he assured me in the case that I don’t like it, he’ll make me a new one for free. Honestly, I wouldn't lose anything so I went with it. When I picked up my fancy drink, I took one sip and it was one of the most disgusting things I have ever tasted! The barista saw the face I made, laughed and began to make a double chocolate chip frappe for me. Anyway, this could have easily happened at any other Starbucks but that’s not where I’m headed. The staff here, at every angle, is welcoming, on your side and eager to help. Another instance I had was meeting Dr. Jennifer Hackney-Price. Before I transferred to ASU West, I had briefly met her at a STEM Open House and I immediately liked her. She is an enthusiastic, kind, intelligent and awesome person that I am grateful to know. A couple of weeks ago, we had a one-on-one conversation about her career and she gave me genuine advice. She has also helped me throughout my project and reassured me that it’s okay to make mistakes. I truly appreciate her because she doesn’t tell me she cares, she shows me. She is someone who has made an impact in my life and I have known her for less than 4 months! Now, that’s not to say she is the only one who cares for her students, there are others who are as happy to help. A few others that I can think of are Pamela Marshall and Jennifer Broatch. With that said, the people (students, professors, staff, etc.) on West campus are so welcoming, assuring and reliable. Since I started, I have not had a bad experience with anyone. Honestly, I feel welcomed here and I am happy to say that I am a part of ASU!

Figure 1. The entrance of Arizona State University West Campus.

Figure 2. A water fountain located outside the University Center Building.

1,415 Miles Away...

At the beginning of my spring semester at Phoenix College, a friend of mine, Sam,

told me she was applying to summer internships and advised that I should, too.

After hearing this, I took it to my advantage and applied to about 7 summer

programs ranging from The University of San Francisco to The University of Iowa

(U of I). Out of the 7 internships I applied for, the first 4 schools rejected my

application. As one would imagine, I was beginning to lose hope. However, after

a week or so, I received a call from U of I telling me that I was accepted. From

the time of the call (March) to May, I was looking for a mentor, filling out

paperwork and practically preparing myself for the 8-week program.

Today, I am 1,415 miles away from home and this is the first time I am completely

on my own. Nonetheless, I have been in Iowa City, IA for 3 weeks and it has been

a great experience so far. The wonderful people, my research project and beautiful

campus have made my stay worthwhile. In my next post, I will be sure to blog about

my research once I fully understand it and am able to explain it!

Figure 1. O'Hare International Airport located in Chicago, IL.

Figure 2. The University of Iowa campus. The building that is shown is known as the Old Capitol.

Figure 3. A closer look at The University of Iowa's Old Capitol

Figure 4. A rainbow outside of my dorm is formed after a day of rain.

Figure 5. The 2018 summer interns at The University of Iowa's SROP (Summer Research Opportunity Program).

Onto the Next Experience...

This was the final week I was a STEM/ TRAIN intern at Phoenix College. During my last week, I did a poster presentation at Metro Tech High School. To be honest, I wasn’t expecting many people to attend since teachers didn’t show up for work due to the RedForEd protests. However, to my surprise, nursing students, along with other faculty, showed up to see our presentations. As a result, the turn out at Metro Tech was great: there was an audience, the food was delicious and everyone seemed to have a good time. I am so grateful for having the opportunity to conduct research at Phoenix College but it doesn’t end here… I will continue at ASU West next semester! I am excited for what the future holds and I wish my fellow interns the best of luck during their journey called life.

Figure 1. The amazing people I met and had the privilege to work with. I would like to thank each and everyone of them for having my best interest in mind and contributing to my wellbeing in one way or another. The order of the people from top left to top right is: Amanda Chapman, Joshua James, Mario Diaz, David Ortiz Leon, Luisa Zamora, RJ Mabry, Ibrahim Ibrahim, Brenda Arvizu (me) and Matt Haberkorn. From the bottom left to the bottom right is: Samantha Gonzalez Faltermeier, Rolanda Bell, Cathy De Veyra and Jasmine Patricio. Again, to each person, thank you for being there for me.

Exciting News

I presented at the ASU West Symposium and ANAS Conference last week. Even though ASU West Symposium was quite slow, it did prepare my mind for the next day: ANAS Conference! I was so excited to travel to Las Vegas for this presentation. I had such a great time with fellow interns and mentor as we explored downtown Las Vegas and the University of Nevada. The poster presentation went well, even though I hardly had anyone at my poster (very sad). All in all, I am much more confident presenting my research at Metro Tech High School next week since I have done so twice.

Figure 1. Sharing my research about unknown bacteria in creosote bushes at the ASU West Symposium.

Figure 2. Presenting my research project at the ANAS Conference at the University of Nevada.

Final Poster

The semester is coming to an end and I forgot to mention my results for this research project. After looking at our data, the rural group had twice as many bacterial groups compared to the urban. In addition, the average number of Colony Forming Units (CFU) of the urban samples differed by about 70% (Figure 1). However, there is no significant statistical difference between bacterial species in urban and rural areas. More research and samples will need to be gathered in order to determine a statistical difference between the two groups. Other than that, I am content with my poster (Figure 2) and am excited to present at the University of Nevada! I wish my fellow interns the best of luck during their presentations and I hope we have a fun, safe trip!

Figure 1. The rural samples have a greater number of CFUs vs. the urban group and a slightly higher group diversity (2 more groups than urban).

Figure 2. Final poster for the Spring 2018 research project. 

Semi-Finished Poster

I seriously enjoy working on anything that involves presentations! I love making posters unique, nice to look at and easy to read. I’ve mentioned this before but I think this has to do with my past experience with graphic design. I definitely paid close attention towards this poster when it came to color, font, text size and text placement. (Figure 1). Unfortunately, I am not too sure about the color because it looks very similar to last year’s and I wanted to switch it up. Also, the placement of the results has not convinced me. I will continue editing and will post the final product!

Figure 1. My 2018 research poster (that may still need corrections).

Slow Weeks

To be honest, for the last couple of weeks, I have had difficulty writing blog posts about my research. I have not been performing DNA extraction since the first 2 extractions because they had similar results. Also, I am unable to perform PCR because I do not have the PCR primers. The primers (27F/1492R, V3F/V3R, V6F/V6R) were ordered this week and should be here in a couple of weeks. Once they arrive, I will then be able to perform PCR, continue my research and hopefully identify the unknown bacteria. In the meantime, I have been editing my research poster to present at the Arizona-Nevada Academy Conference on April 21, 2018.

Figure 1. The Arizona-Nevada Academy of Science and the Arizona/ Southern Nevada Branch of the American Society of Microbiology will host the 62nd meeting at the University of Las Vegas ("Joint Science...", n.d.). 

Joint Science and Mathematics Meeting. (n.d.). Retrieved April 05, 2018, from https://www.aznvas.org/meeting/details/

Possible PCR Primers

I was able to narrow possible PCR primers down to about 3 pairs. It turns out, I do

not have to necessarily make my own primers, I can use primers that have already

been created to test them out. With this in mind, after researching universal primers,

I have decided to use a pair of PCR primers from last semester and 2 new ones. The

ones from last semester were 27F and 1492R. The primers I want to test are V3F,

V3R, V6F and V6R. Each primer has a specific sequence that will be replicated and

it can be seen in Figure 1. I found it interesting that the new primers have lowercase

letters in their sequence. After researching why this could be, thinking it could have

possibly been a typo, I found that lowercase letters can mean “low-complexity or

repetitive elements” (“Legend: Fasta”, n.d.).

Figure 1. The possible PCR primers that I plan to use during PCR. There are 6 in total, equaling 3 pairs. The sequences are listed next to each one starting from 5' and ending at 3'. 

Legend: Fasta. (n.d.). Retrieved March 30, 2018, from https://www.ncbi.nlm.nih.gov/SNP/snp_legend.cgi?legend=fasta

Chakravorty, S., Helb, D., Burday, M., Connell, N., & Alland, D. (2007). A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. Journal of Microbiological Methods, 69(2), 330-339. https://doi.org/10.1016/j.mimet.2007.02.005

PCR Primers

This week was quite slow because I have been researching possible PCR primers to
use for Polymerase Chain Reaction (PCR). The next step of my research is to
perform this but I cannot do so without these primers. With that said, I have to
develop my own primers from researching articles and protocols.. Even though I
am looking for universal primers, it is a little difficult to determine which one
would be best because certain ones work for certain bacteria or environments.
Since I am trying to identify unknown bacteria, I will most like have to develop
more than one primer. For example, one primer for gram positive bacteria and
another for gram negative bacteria. I will continue my research and hopefully
begin PCR next week!

Figure 1. The materials and process of Polymerase Chain Reaction (PCR). During PCR, the specific DNA that the primer targets is replicated over and over. If the primer cannot find that DNA, it means the sample does not have it and vis versa. ("PCR", n.d.).

PCR. (n.d.). Retrieved March 23, 2018, from
http://ib.bioninja.com.au/standard-level/topic-3-genetics/35-genetic-modification-
and/pcr.html

Preparation of Research Poster

I started to prepare my poster for the upcoming research presentations. A few of them that I hope to present at will be the Estrella Mountain Conference, ASU Symposium and Arizona-Nevada Academy of Science Conference. I have already included items such as the hypothesis and abstract but still need to include my data. For instance, I have to provide a map that includes the locations each unknown sample was taken from (attached below). In addition, most of the bacteria from last semester’s were categorized in bacterial group numbers (attached below). I will make sure to upload my poster once I have it completed!

Figure 1. The 5 locations where creosote unknown samples from last semester's research project were obtained. The different colors match with the stars on the following maps and shows where it is. In addition to the location, the group number and locality is included. Rural (R) samples had to be further than 4 miles from populated areas and Urban (U) where within 4 miles of a populated area.  

Figure 2. The legend to the following maps that display the location of the creosote bush unknown samples. This also shows the total population per square mile by different shades of color.

Figure 3. This map displays the city of Phoenix. There are four unknown creosote samples that were obtained throughout this city. The samples, from left to right, were from White Tank Mountain, Phoenix College, Tempe and Coolidge. 

Figure 4. This map displays the city of Tucson. There is only one unknown creosote sample that was obtained from this city. The sample was from a suburban area in Tucson. 

Second DNA Extraction

This week, I performed the second DNA extraction on the unknown Larrea Tridentata bacteria. I was unsatisfied with the results I obtained a couple of weeks ago because the NanoDrop DNA values were low (well, at least to me). Due to these results, I thought I had done something wrong. With this in mind, I was hoping to get higher amounts of DNA during this extraction. However, that was not the case because I practically had about the same amount of nucleic acid. After this extraction, nothing changed and I will be using these samples for PCR. Below is the nucleic acid graph and data table for this second extraction (Group B).

Figure 1. The NanoDrop data collected from unknown bacteria in creosote bushes (group B). Five DNA extracted samples were used: A1, A8, A24, A26 and A27. Displayed with each bacteria is the amount of nucleic acid, 260 ratio, 280 ratio and260/280.

Figure 2. The NanoDrop graph from unknown bacteria in creosote bushes. The five displayed DNA extracted samples, A1B, A8B, A24B, A26B and A27B, are shown, along with the wavelength and the absorbance.

Fun Facts About Larrea Tridentata

Larrea Tridentata, also known as creosote bush, is a common shrub located around Southwestern United States and Northern Mexico (Arteaga, 2005). These particular lands are known for their warm deserts, which is where this plant is most abundant because extreme freezes, even though they can occur in these areas, limit its distribution. Larrea Tridentata is also “used to treat a variety of illnesses including infertility, rheumatism, arthritis, diabetes, gallbladder and kidney stones, pain and inflammation” (2005). Even though this range extends to about 50 other illnesses, it is most commonly used in “diseases of gynaecologic and renal origins” (2005). In addition, it is useful in fighting “against bacteria, viruses and parasites, both internally and externally” (2005). Though this plant seems to have an enormous amount of benefits, “most of the medicinal uses of Larrea tridentata are not supported by experimental or clinical studies” (2005). Additionally, there are disadvantages associated with this plant. For example, “creosote bush is unpalatable to livestock and most wildlife [becomes] toxic, sometimes causing death” (2005). To support this, pregnant ewes (sheep) “have been reported to die after eating the leaves” (2005). Another unfortunate case involves a “patient develop[ing] hepatitis 2–3 months after beginning daily consumption of creosote bush leaf (proven by biopsy)” (2005). Larrea Tridentata has been associated with various medicines that have made an impact in the life of individuals while at the same time negatively affecting organisms.

Figure 1. This "Arizona Natural" dietary supplement is made from Larrea tridentata. However, these capsules "are not intended to diagnose, treat, cure or prevent any disease" ("Arizona Natural...", 2015).

Reference:

Arizona Natural Resource Chaparral Dietary Supplement 500 mg. (2015). Retrieved February 22, 2018, from https://www.vitalitymedical.com/arizona-natural-resource-chaparral-dietary-supplement-500-mg.html

Arteaga, S., Andrade-Cetto, A., & Cárdenas, R. (2005). Larrea tridentata (creosote bush), an abundant plant of Mexican and US-American deserts and its metabolite nordihydroguaiaretic acid. Journal of Ethnopharmacology, 98(3), 231-239. https://doi.org/10.1016/j.jep.2005.02.002

Unknown Bacteria NanoDrop Data

Using the unknown extracted DNA samples from last week, I ran them in the NanoDrop and have included the results below. Figure 1 shows the amount of nucleic acid found in each unknown and it’s purity (the 260/280 ratio should be around 1.7 to be considered pure). From looking at the table, I was hoping to get higher amounts of DNA (above 600). Due to this, I will continue to perform the QuickExtract Bacterial DNA Extraction to yield higher quantities. Nonetheless, the samples remained around the 1.7 260/230 ratio, which I am happy about. In addition, Figure 2 shows the ideal dumbbell shape the wavelength of the samples produced.

Figure 1. The NanoDrop data collected from unknown bacteria in creosote bushes. Five DNA extracted samples were used: A1, A8, A24, A26 and A27. Displayed with each bacteria is the amount of nucleic acid, 260 ratio, 280 ratio, 260/280 ratio and 260/230 ratio.

Figure 2. The NanoDrop graph from unknown bacteria in creosote bushes. The five displayed DNA extracted samples, A1, A8, A24, A26 and A27, are shown, along with the wavelength and the absorbance. 

Starting Slowly...

I found my lost DNA samples from last semester! For those of you who may not know, during my Fall 2017 research project, my extracted unknown DNA samples went missing and I could not find them anywhere. However, today, I so happened to be looking inside the biohazard freezer and dug under the items that were in there. I was initially looking for QuickExtract bacterial DNA but luckily, I also ran into my missing samples! Even though the mystery has officially been solved, I could no longer use these samples so I had to throw them away. Other than that, I began to perform DNA extraction on new unknown bacteria from creosote bushes. These samples were obtained by a fellow intern, Luisa Zamora, who is also working on this project with me. Slowly but surely, I hope we will make significant progress!

Figure 1. The missing extracted unknown DNA samples that were lost during my Fall 2017 research project. 

Figure 2. Unknown bacteria inside TSB broth before 24 hours.

Figure 3. Unknown bacteria inside TSB broth after 24 hours.

Larrea tridentata Research Project

The research I will conduct this semester involves identifying unknown bacteria from Larrea tridentata, also known as creosote bush. Various tests will be used to help determine and put a name on present bacteria. This is a continuance of last semester and because my previous DNA samples were lost, I will have to start over. It’s quite ok that this occurred because repeating procedures is great practice. I know for a fact this will benefit and enhance my skills in a research laboratory. In addition, I began working on my research proposal and will most likely have it posted next week. I cannot wait to begin my project and share my findings with you all!

Figure 1. This is a 10X magnification of a pedicel from a rose. Maybe if I'm fortunate enough, I will find a bacteria that looks just as beautiful! (Gracewood, 2010)  

Gracewood, P. (2010, August 9). Shadows On Stone. Retrieved February 01, 2018, from http://shadowsonstone.blogspot.com/2010/08/sculpture-and-eckhard-volcker.html

New year, new opportunities!

I am so excited to be back at S-STEM because I genuinely enjoy myself there. The friendly atmosphere and the help I receive from my mentors allow me to feel at ease. Also, S-STEM has now merged with TRAIN and fortunately, I will have the chance to continue enhancing my research skills and knowledge at ASU West. With this in mind, I am happy and proud to say that I have been accepted to this school and will begin there Fall 2018! I am definitely looking forward to what the future holds. Aside from that, this will be my last semester at Phoenix College but I am eager to meet many of the new interns.

Figure 1. It's official, my Arizona State University acceptance letter!