April 26

Lab 14 (04/25/19): Revising

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Objective:

The objective of this lab was to be able to review the information. This lab was also useful to be able to collect all the information into one spread so all the information can be compared to each other. This lab was also used to have one more review over abstracts and posters.

Procedure:

In order to be able to do this we had to use the information that we had previously recorded and add that to a group excel sheet. In order to revise the documents that we had to submit we had to open them and revise them as a group in order to be able to make as many correction as we could.

Conclusion:

In conclusion this lab was useful to put all of our metadata in one place so that it may be easily accessible. Editing our abstract and poster, was useful because it ensures that our information is reliable and well written.

Future Observations:

Having this lab to revise and edit our information is helpful because it remind us that revision is something that needs to be done constantly. Therefore, this lab is something that will keep us in the habit of revising and editing constantly

 

 

Metadata

Name: Jessica Mann

Section: 25

Group: 1

Soil ID: JGM25_1Sp19

GPS location: -97.1200, 31.5500

Tree species: unknown

BDH: 11.43 cm

pH: 7

Soil texture: silt

Extraction method: Chelex

DNA concentration: 78.0

Volume ul: 100

PCR: –

Soil Label: JGM25S19

 

Abstract and Title

 

Soil eDNA and Ciliate Culture DNA Extraction and PCR Amplification

Abstract

Not much research has been done on the topic of soil ciliates. Therefore, a thorough research experiment on the study of soil ciliates’ DNA is necessary. This experiment was conducted to determine the diversity of ciliates from soil samples collected from the rhizosphere of different trees on the Baylor campus. We collected the metadata of the samples, such as tree and soil type, location, soil pH and percent water content. The silica bead eDNA extraction protocol and the Chelex DNA extraction from Ciliate culture were run on separate samples. We then ran gel electrophoresis, quantified the extracted DNA using Nanodrop and attempted to amplify the 18sV4 region using PCR. Gel electrophoresis yielded DNA bands for both extraction methods, however the gel run from the PCR reaction failed to produce results for either sample. Nanodrop showed that there were higher DNA concentrations for the silica bead extraction sample compared to the Chelex extraction samples. Due to the negative results for PCR amplification, DNA sequencing will not be performed on these samples.

Category: Jessica Mann-33 | LEAVE A COMMENT
April 26

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Shivam Patel 4/25

Purpose:  The purpose of the lab was to create abstracts for our poster and finish our posters, as well as label and sort our soil.

Procedure:

1. Label soil bag with your sample ID.

2. Fill in the excell spreadsheet with information of your sample.

2. Finalize abstract and poster.

Abstract:

Ciliates are unicellular eukaryotic organisms that reside in freshwater or soil ecosystems. Ciliates are an important factor within the ecosystem because they consume different bacteria and protozoa, and act as a source of nutrition for organisms at higher trophic levels. The enormous discrepancy between the amount of research conducted on ciliates living in marine biomes versus ones living in the soil is due to a general lack of interest and/or knowledge of their importance. This experiment was conducted over the course of fourteen weeks in an effort to fill the gap between the amount of information known about marine and soil biodiversity by determining the overall composition of ciliates living in the rhizosphere of different trees across Baylor University’s campus. The V4 region of the 18S rRNA was observed because it is conserved within all eukaryotes and is unique to each specific organism. Soil samples were collected from the rhizosphere, where the highest concentration of ciliates are presumed to inhabit because of its abundance of nutrients and gas availability. After collection, the soil was searched for the presence of ciliates. Once the ciliates were isolated, their DNA was extracted and purified. The pure DNA was amplified through a polymerase chain reaction and ran through gel electrophoresis to determine whether or not eukaryotic DNA was present. Although our sample contained a very minute amount of DNA, if substantial DNA had been found, it would be sequenced using an online bioinformatics platform- QIIME2, to determine the specific organisms in our sample.

Conclusion: With our poster and abstract finished, now we just need to prepare to present at the symposium.

Category: Shivam Patel-34 | LEAVE A COMMENT
April 26

Lab#14

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Purpose:

The purpose of this lab was to begin preparing for the CURE Symposium which will take place next Friday. We prepared our poster for printing and created abstracts that will be printed into the pamphlet for the event. Also during this lab we organized our soil metadata into a spreadsheet.

Material:

  • Computer with internet connection.
  • Previous notebooks.
  • Soil Bag.
  • Post-PCR DNA Sample.
  • Poster.

Procedure:

  1. Vote on logo for t-shirt and /or stickers.
  2. Collect sample ID.
  3. Enter metadata into spreadsheet and if PCR was positive, more it to the appropriate spot and place soil bag in container.
  4. Go to the computer lab and review poster, and make necessary changes.
  5. Discuss abstract and combine ideas to make final abstract.

Data:

Soil eDNA Metadata Spreadsheet:

Group Members: A.J. Alvarez, Megan Cordova, and Jessica Mann.

Section: 25

Group: 1

Soil ID: AA25_1Sp19

GPS Location: (-97.1136,31.5445)

Tree Species: unidentifiable

pH: 6.9

Soil Texture: Silty Loam

Extraction Method: Silica Bead

DNA Concentration ng/microleter: 479.5

Estimated Volume: 50

PCR: –

Soil Label on Bag: AA25SP19

Abstract:

Not much research has been done on the topic of soil ciliates. Therefore, a thorough research experiment on the study of soil ciliates’ DNA is necessary. This experiment was conducted to determine the diversity of ciliates from soil samples collected from the rhizosphere of different trees on the Baylor campus. We collected the metadata of the samples, such as tree and soil type, location, soil pH and percent water content. The silica bead eDNA extraction protocol and the Chelex DNA extraction from Ciliate culture were run on separate samples. We then ran gel electrophoresis, quantified the extracted DNA using Nanodrop and attempted to amplify the 18sV4 region using PCR. Gel electrophoresis yielded DNA bands for both extraction methods, however the gel run from the PCR reaction failed to produce results for either sample. Nanodrop showed that there were higher DNA concentrations for the silica bead extraction sample compared to the Chelex extraction samples. Due to the negative results for PCR amplification, DNA sequencing will not be performed on these samples.

Poster:

Conclusion:

In conclusion today’s lab had mostly to do with finalization. Since the semester is coming to an end, we are trying to prepare us for our final presentation next week. We finished up our posters as well as created our abstracts and I am feeling more comfortable when talking about the contents of my poster and the research we did this semester.

Future Steps:

In future labs I would like to practice presenting our poster and next Friday we will be presenting the research we did throughout the semester. I would also like to continue to run the metabarcoding so we can continue to look at the amazing diversity of Eukaryotas in the soil sample.

Category: A.J. Alvarez-31 | LEAVE A COMMENT
April 26

Lab #14 Poster Presentation and Abstract Submission 4-25-18

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Objective: To finalize the metadata from our samples, chose the samples to get sequenced, and submit our Abstracts, Titles, and Posters.

Procedure: 

1. Vote on the Cilicure Logo

2. Input Metadata for sample on spreadsheet

3. Label sample

4. Review abstract and title and poster in the computer lab

5. Submit Title, Poster, and Abstract

Data: 

Metadata:

section group label GPS location species BHD pH Soil texture Extraction DNA concentration PCR
25 1 MKC25_1Sp19 -97.123215, 31.545735 Live Oak 19.25 cm 7 clay loam Chelex 183.0 –

Title:

Soil eDNA and Ciliate Culture DNA Extraction and PCR Amplification

Abstract:

Not much research has been done on the topic of soil ciliates. Therefore, a thorough research experiment on the study of soil ciliates’ DNA is necessary. This experiment was conducted to determine the diversity of ciliates from soil samples collected from the rhizosphere of different trees on the Baylor campus. We collected the metadata of the samples, such as tree and soil type, location, soil pH and percent water content. The silica bead eDNA extraction protocol and the Chelex DNA extraction from Ciliate culture were run on separate samples. We then ran gel electrophoresis, quantified the extracted DNA using Nanodrop and attempted to amplify the 18sV4 region using PCR. Gel electrophoresis yielded DNA bands for both extraction methods, however the gel run from the PCR reaction failed to produce results for either sample. Nanodrop showed that there were higher DNA concentrations for the silica bead extraction sample compared to the Chelex extraction samples. Due to the negative results for PCR amplification, DNA sequencing will not be performed on these samples. 

Poster:

Conclusion: 

We will present our poster at the Cure Symposium on Friday from 2-4. Since we got negative results for the PCR reaction, our sample will not be sequenced. We will still present our negative results and observe the other posters at the CURE Symposium.

Category: Megan Cordova-31 | LEAVE A COMMENT
April 26

Lab 14: Poster Presentation and Abstract Submission

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Daphne Simo

04/26/19

I. TITLE

Poster Presentation and Abstract Submission

II. RATIONALE/PURPOSE

The purpose of this lab was to create a finalized version of of our abstract and scientific poster to present at the CURES in Bio Symposium next week. We also completed a spreadsheet that contained metadata for our selected soil samples used for extraction, purification, amplification of the environmental DNA.

III. MATERIALS

Computer

Poster

Abstract

IV. PROCEDURE

Metadata Collection and Soil Sample Labelling

  1. Label bag and eDNA with your Soil Sample ID.
  2. Complete the “Soil eDNA Metadata Spring 2019” spreadsheet with the soil sample ID,  pH, volume of DNA, PCR results, DNA concentration (ng/μl), Breast Heigh Diameter, GPS location, soil texture, and Genus species of the tree where the soil was collected.
  3. Complete questionnaire on QTM about t-shirt designs for Cili-CURE and availability to present at the symposium.

Abstract and Scientific Poster Editing

  1. Work with group members to edit and finalize abstract and scientific poster for submission.
  2. View feedback from Dr. Adair and the LA/TA to improve abstract and poster.
  3. Submit abstract and poster to Box and for Week 14 QTM.

V. DATA/OBSERVATIONS

Metadata

Group Members

Tyler Kingston, Daphne Simo, Johanna Warner

Section

21

Group Number

4

Soil ID

KSW21_4Sp19

GPS Location

-97.1146, 31.532

Tree Species

Quercus imbricaria

BHD (cm)

34

pH

6.5

Soil Texture

Clay Loam

Extraction Method

Silica Bead

DNA Concentration (ng/μl)

244

DNA Volume (μl)

15

PCR Results

+

Soil Label on Bag

KSW21SP19

 Column

Title of Poster and Abstract

Extraction of environmental DNA from the soil rhizosphere of Shingle Oak tree

The soil rhizosphere of trees have an abundance of ciliates and microorganisms present that have not been subjected to extensive research to analyze their diversity. Ciliates are a group of protists that are distinguished by the absence or presence of cilia. Ciliates are vital in the rhizosphere ecosystem mainly as predators. The purpose of this study was to evaluate the biodiversity of ciliates presence in the rhizosphere of trees on the campus of Baylor University. To determine this, a soil sample was collected at a specific site behind the Student Life Center. The soil sample was then used to find its ph, percent water content, and soil texture. An effective protocol was created to extract and purify DNA from the soil. It included silica beads to break up the cells, charcoal to bind to impurities, and isopropanol was used to purify the DNA using a vacuum. DNA was successfully found from the soil sample and the 18s V4 region was amplified. From there, the future goal is to determine the sequence of the DNA.

Poster

VI. STORAGE 

Our finalized abstracts and posters were submitted to Box for future printing.

VII. CONCLUSION

Despite being our second-to-last lab, I believe it was one of the most rewarding session yet. I was able to see all of the work I have done with a single soil sample from campus such as having the ability to extract and purify its DNA and performing a polymerase chain reaction and gel electrophoresis on the eDNA we were able to collect. Furthermore, I have seen advancement in my ability to express my scientific research through writing an abstract and curating a scientific poster.

VIII. FUTURE STEPS

Moving forward, I hope to review all of the processes we have performed on our soil sample this semester and prepare to present my research at the CURES in Bio Symposium in the coming week.

Category: Daphne Simo-31 | LEAVE A COMMENT
April 26

Lab 14: Abstract and Poster

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Sydney Ortenberg

April 26, 2019

Lab 14: Abstract and Poster

Purpose:

The purpose of this lab was to improve our abstracts and posters for the Cili-CURE symposium. We also needed to vote on a logo and enter our information into the dropbox and class spreadsheets.

Procedures:

  1. vote on logo
  2. write down identifier on test tube
  3. record metadata on shared excel sheet
  4. work on abstract and poster
  5. upload abstract and poster to Dropbox

Data:

Soil ID: LOS22_3Sp19

GPS Location: -97, 30

Tree Species: Quercus Virginiana

BHD: 140cm

pH: 6.0

Soil Texture: sandy loam

Extraction: Silica Bead

DNA Concentration: 96ng/uL

Volume: 500

PCR: positive

Soil Label: SLO s2019

Abstract:

Ciliates play a major role in the food web which impacts all hierarchies of life. There is vast biodiversity in the rhizosphere of Earth, containing ciliates and other microorganisms (1). Little is known about the abundance of organisms that reside in the soil of terrestrial environments. This study was conducted to determine the diversity of soil ciliates in the rhizosphere on Baylor University’s campus. The process included collection, extraction, and amplification of ciliate DNA from the soil samples (2). The sample was retrieved from a Quercus Virginiana tree on Baylor’s campus in sandy loam soil. Our PCR for the 18S V4 primer resulted in a positive DNA band although the DNA concentration was not completely pure. Our results indicate that there is a large concentration of ciliates in the rhizosphere of trees on Baylor University’s campus.

Title: Investigating Soil Ciliate Biodiversity

Storage: Data tubes were placed back on the rack.

Conclusion and Future Steps:

This lab allowed us to wrap up some things before we have our presentations and the symposium. We needed to record all of our data on the class spreadsheet so it is all organized and all of the data is in one place. We also took feedback from our TA and LA’s to improve our abstract and poster so they can be printed. As a group, we all edited our abstract and poster to make it better. We also voted on a logo for a sticker or T-shirt so we can always represent Cili-CURE throughout Baylor. In the future, the posters will be printed and we will have the CURE symposium in which we will show our posters and also have a presentation in class.

Category: Sydney Ortenberg-34 | LEAVE A COMMENT
April 26

Biology 1106: Lab #14: Poster Presentation and Abstract Submission

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Garrett Darden

Biology 1106-Section 25

Dr. Adair

4/26/2019

CILI-CURE Lab #14: Poster Presentation and Abstract Submission

Objective: The objective of lab this week was to begin preparing for the CURE Symposium which will take place next Friday. We did that this week by once again correcting our posters, writing our abstracts, and organizing our soil metadata into a spreadsheet.

Purpose: The purpose of this lab was to set everything logistically in place for CURE Symposium next week, like prepping our posters for printing and creating abstracts that will be printed into the pamphlet for the event. The second purpose was for us to once again look at our older data and to create an abstract as well as further improve our posters  

Materials: 

  1. Computer with Internet Connection
  2. Access to Prior Notebooks
  3. Soil Bag
  4. Flask with Post-PCR DNA Sample
  5. Access to Copy of Poster
  6. Access to Writing Program like Word or Google Docs for Writing the Abstract

Procedure: 

  1. Open up your computer and follow the metadata link to the metadata spreadsheet
  2. Use your group members, soil bags, post-PCR DNA sample flask, and older notebooks from online or your personal notebook in order to fill out all of the blanks on the spreadsheet.
  3. Look up older data like GPS coordinates, BHD, the nanodrop data, tree species, soil and pH assays, and the soil bag ID and the estimated volume of post-PCR DNA sample flask
  4. Once all of the data is tranferred over to the spreadsheet, return the soil bags and DNA sample flask to their respective containers, and clean up the lab space and move to a computer lab for the next steps.
  5. Prior to the lab, draft abstracts should have been made by each individual member of the group, so now pull up each draft and work together in order to combine the three into one abstract that will represent the whole group and aim to have the draft be at max 250 words.
  6. Now ask your TA’s and instructor what suggestions and critiques they have of your poster and be sure to write them down so that they can be corrected later.
  7. Whether or not the title is changed, put the final title of the poster with the final abstract and upload the paper to the designated BOX folder as well as too Canvas under the QTM 14 assignment.
  8. Once that is finished then work as a group in order to address the suggestions and critiques given by your TA’s and instructor in order to improve and fix the poster.
  9. After all comments and suggestions have been addressed and the poster is finished, upload the file to the BOX folder so that it can be printed for next week.
  10. Shut down the computer and complete the paper QTM and turn it in to your TA’s prior to leaving the lab and clean up your lab space prior to leaving.

Results/Data: 

Soil eDNA Metadata Spreadsheet:

Group Members: Garrett Darden, Caleb Touchstone, and Chris Amezcua

Section: 25

Group: 2

Soil ID: ADT25_2Sp19

GPS Location: (-97.1136, 31.5445)

Tree Species: Quercus Virginiana

BHD (cm): 44.03

pH: 4.1

Soil Texture: Clay Loam

Extraction Method: Silica Bead

DNA Concentration ng/microliter: 250.2

Estimated Volume: 50

PCR: +

Soil Label on bag: CT25Sp19

Final Title and Abstract:

Title:  Analysis of eDNA from a Soil Sample in the Search for Soil Ciliate DNA

Abstract: Soil ciliates are crucial organisms in the rhizosphere as they perform many important roles contributing to soil health. Currently, research concerning topics related to soil ciliate diversity is limited. Conventionally, ciliates have been identified and categorized through morphological characteristics and behaviors due to a lack of a standard genomic method for easy identification. This study aims to explore a standard method for ciliate identification through metabarcoding. For this, soil was collected and environmental DNA was extracted using the Silica Bead grinding method followed by Column Purification. Polymerase Chain Reaction was used to amplify the V4 region of the 18s rRNA subunit. Gel electrophoresis results showed that PCR amplified the eDNA. The image taken of the gel showed a concentrated band of DNA from the eDNA sample. Nano-drop analysis of the eDNA showed a 250.2 ng/ml of the DNA while it had a purification of 1.46 A260/280. The eDNA extraction method conducted appears to be the best option for extracting DNA due to the amount of DNA replicated. Metabarcoding of the V4 region of the 18s rRNA subunit was conducted using the eDNA to identify what kind of ciliates were extracted from the environmental sample and sequence. Bioinformatics (Cyverse/QIIME2) will be used to analyze how successful the V4 region can be in the identification of ciliates.

Copy of the Poster: 

 

Conclusion: In conclusion,  I believe that this week was insanely productive because we were able to put the finishing touches on the poster as well as create our abstracts. I also began to feel more and more comfortable talking about the content of my poster to others when talking through it for suggestions and critiques

Future Goal: In future labs I want to continue improving my poster creation and abstract writing skills so that I can continue to deliver research quality work for such events as CURE Symposium and  and Scholar’s week. I also want to be able to continue running metabarcoding so that we can continue to look at the diversity of the eukaryotes in the soil sample to a deeper degree, more so than we have in the past few weeks while working with Qiime2 and CyVerse.

Category: Garrett Darden-31 | LEAVE A COMMENT
April 26

Lab 14

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Lab 14

04/25/2019

Andreea Loghin

Objective:

The objective if this lab was to edit the poster and write the abstract for the Cures Symposium as well as contribute to the comprehensive spreadsheet with data about our DNA sample and tree and soil metadata.

Purpose:

The purpose of this lab was to give us a better understanding of what it means to participate in a scientific poster presentation and what the standards are for such posters as well as determine which DNA sample is viable to be sent for future analysis.

Procedures:

  1. Lable vile with sample identifier (GLR22_7Sp19)
  2. return tube to cooler
  3. add data about latitude and longitude, tree diameter, pH, soil texture, methods of extraction, PCR results, DNA concentration, volume to the spreadsheet
  4. work on poster
  5. write abstract

Results:

SOIL eDNA metadata:

Group members: Sara Rothrock, Rebekah Gerry, Andreea Loghin

Section: 22

Group: 7

SOIL ID: GLR22_7Sp19

GPS location: -97.1195413, 31.5495435

Tree Species: Quercus virginiana

BHD (cm): 55.0064

pH: 6.5

Soil Texture: Loamy sand

Extraction Method: Silica Bead

 

Abstract: 

There are many standard methods for extracting Ciliate eDNA but not all are effective and cost efficient.

Ciliates are protozoa in the Kingdom Protista. They play many different roles within soil and aquatic ecosystems. There has been very little research done on ciliate behavior and interactions within the soil. Our study targeted ciliates within the rhizosphere. The rhizosphere plays a key role in the cycling of nutrients as well as plant growth. Ciliates shape the diversity of microorganisms within the rhizosphere, thus their presence is vital to a healthy ecosystem.

The purpose of this study was to investigate new methods for eDNA extraction of ciliates.

Creating this new method was achieved by researching different ways to extract eDNA. These different methods were then combined to maximize the amount of eDNA collected. Metadata was collected regarding the soil sample and the environment it was collected from. Gels were run to determine the amount of DNA collected. The samples that contained an abundance of DNA underwent PCR in order to amplify the strand so they could more easily be sequenced.

The samples were loamy sand, with a pH of 6.5. The concentration of DNA in the sample was 1125 ng/ul and the A260/A280 value was 1.33. The DNA sequenced not only belonged to ciliate species, but fungal and bacterial species as well.

These results gave reason to believe the use of charcoal and Silica beads was effective in the extraction of DNA.

 

Poster: click here

 

Future Goals:

In the future, we hope to get more data about the DNA samples that will be sent off for future analysis as well as present our poster during the CURES Symposium. We hope to contribute to the scientific community with valuable information regarding DNA extraction methods since we developed novel ways to do that.

Storage:

DNA samples were stored in the cooler after they were labeled. Everything was taken off the lab tables.

Category: Andreea Loghin-32, Uncategorized | LEAVE A COMMENT
April 26

Lab 14: Poster Presentation and Abstract Submission

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Leslie Morales-21

 

Objective:

The purpose of lab today was to finalize our abstract and edit our poster so that they can be sent off to be printed.

Procedure:

  1. Vote on logo for t-shirts and/or stickers
  2. Collect sample ID
  3. Enter metadata into spreadsheet and if PCR results were positive, move tube to appropriate rack and place soil bag in tub.
  4. Go to computer lab and review comments on poster and make necessary edits.
  5. Discuss abstracts and combine different ideas to form a final abstract.

Data:

 

Metadata

Group members: Leslie Morales, Holli Brown, Haleigh Inthavong

Section: 21

Group: 3

Soil ID: BIM21_3sp19

GPS location: -97.1168, 31.5502

Tree species: Texas Live Oak

BHD (cm): 49

pH: 6

Soil texture: Silt Loam

Extraction method: Silica bead

DNA concentration ng/µl: 598.2

~Volume: 15

PCR: +

Soil label on bag: HMB21S19

 

Poster title

The discovery of eDNA and the importance of ciliate biodiversity

 

Final Abstract

Soil ciliates are greatly understudied and play an important role in the rhizosphere. The objective of our study was to identify the presence of DNA within the soil sample collected from the Baylor University campus trees. The soil sample was collected from the O region of campus where the tree was classified as a Texas Live Oak, and the soil metadata, including a pH of 6, percent water of 6.024%, and soil texture of silt loam was observed and recorded. Following soil collection, students attempted to culture any observed ciliates, DNA extraction was performed by way of silica beads, the extracted DNA was purified through the use of a column and vacuum filtration, and PCR and gel electrophoresis was conducted utilizing the isolated DNA samples. The DNA sample had a 260/280 ratio of 1.42, which indicated that the DNA was relatively pure, and the sample had a positive PCR of approximately 400bp in comparison to the 1 kb ladder signifying that DNA was present within the sample. Because limited researched exists in regards to soil ciliates, the discovery of eDNA within campus trees can potentially lead to more future studies concerning the significance of ciliate biodiversity within the rhizosphere.

 

Final Poster 

Conclusion/ Future Steps:

Today’s lab dealt mostly with finalization. As the semester is coming to an end we are just trying to make sure everything is in place for presentations next week. In the future, we will practice presenting our posters and next Friday we will be in the atrium presenting the research that we have conducted.

Category: Uncategorized | LEAVE A COMMENT
April 26

Lab 14: Poster Edits and Abstract 04/25/19

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Purpose: 

The purpose of this lab was to prepare for our poster presentations by making edits based on comments/critiques made. Another focus was to make a final draft for an abstract that will be submitted for the CURE symposium. We organized all the information (meta-data) from our samples in order to analyze our samples after they have been sequences.

Procedure: 

  1. Vote on CILICURE logo, and what to do with it
  2. Organize metadata into excel sheet
  3. Make edits to poster and submit for printing, upload to box file
  4. Collaborate with team members to make a final abstract that will be submitted

Excel Metadata: 

section group label GPS location species BHD pH Soil texture Extraction DNA concentration
25 4 GRS25_2Sp19 -97.1182, 31.5498 Quercus virginiana 57cm 6.4 clay loam silica bead 262.1
  • The PCR result was also negative

Poster: 

Abstract: 

Title:

Soil eDNA Analysis Targeting the V4 Region Using the 18S Primer

Abstract

Soil ciliates are a diverse group of eukaryotes that play an important role in the environment but are understudied due to a lack of standard methods used to extract them from soil. The purpose of this experiment was to determine ciliate biodiversity in soil samples taken from the rhizosphere of Baylor trees. The protocols used were ones that have yet to be perfected in hopes of establishing them as universal method such as silica bead extraction of DNA and the chelex extraction method. DNA was extracted and purified from the soil collected using the ‘silica bead method’. The DNA concentration was obtained using a nanodrop and gel electrophoresis by running against a mass standard, and used PCR to amplify the 18s V4 region. The Polymerase Chain Reaction yielded a negative result, indicated by a ‘smear’ of DNA rather than a band. The nanodrop showed the concentration of DNA to be 262.1 ng/µl with the A260/280 to be 1.5. Despite negative results, the experiment showed the validity of results that can be found through silica bead and chelex DNA extraction; however, the lack of positive results was most likely due to an improper dilution or a degradation of DNA. Additionally, further research can be done using bioinformatics to visualize the ciliate diversity.

Word Count: 215

Discussion/Future Goals: 

After working through edits for the poster I am becoming more excited to share our research with others. We will continue to practice presentations to the class next week before our presentation at the CURE symposium. Hopefully soon we send our DNA off for Illumina Sequencing and analyze it using QIIME2 and Cyverse. We will be able to use these programs in order to determine the biodiversity of the organisms, and hopefully ciliates, on our soil sample that was collected at the beginning of the semester.

 

Category: Marshall Garcia-31 | LEAVE A COMMENT